I just thought of a distinction regarding subduing the inclination: there are two kinds of inclinations. There is an inclination that is bad in its essence, like hatred of your brother, and there are inclinations that are not bad in themselves, like hunger, sex, sleep, etc. In a case where there are two commandments, like Torah study in a more interesting place and in a less interesting place, there is no advantage to learning in the less interesting place, because the inclination of curiosity is not bad in itself, and therefore there is no point in breaking it. And proof of this is what is written in tractate Nazir:

“As it was taught: Rabbi Elazar HaKappar Berabbi says, what is the meaning of the verse, ‘And he shall make atonement for him, for that he sinned against the soul’ (Numbers 6:11)? Against what soul did this one sin? Rather, it is because he deprived himself of wine. And if this one, who deprived himself only of wine, is called a sinner, then one who deprives himself of everything all the more so.”

We see here that there is no point in breaking the urge to eat.

There is an argument that even in the case of an inclination that is not negative, there is value in breaking it in order to be more autonomous, less driven by impulses. But in principle it seems you are right. Maybe one should add that if you feel that you are being led too much by your inclinations, then you should break even inclinations that are not negative. Obviously there is no value in breaking an inclination in itself unless it creates a problem.
As for the nazirite, there is even a complementary example in Nedarim 9b:

“As it was taught: Shimon the Righteous said, in all my days I never ate of the guilt-offering of an impure nazirite except for one. Once a certain nazirite came from the South, and I saw that he had beautiful eyes, a handsome appearance, and his locks were arranged in curls. I said to him: My son, what did you see that led you to destroy this beautiful hair? He said to me: I was a shepherd for my father in my town. I went to draw water from the spring, and I looked at my reflection, and my inclination surged within me and sought to drive me from the world. I said to it: Wicked one, why do you pride yourself in a world that is not yours, with one who is destined to become maggots and worms? By the Temple service, I will shave you for the sake of Heaven. Immediately I arose and kissed him on his head. I said to him: My son, may there be many nazirites like you in Israel. About you the verse says: ‘When a man shall clearly utter a vow, the vow of a nazirite, to consecrate himself unto the Lord.'”

Oren, there is no basis for the distinction between an inclination with a good essence and one with a bad essence. What determines it is the goal.

(Also, the whole idea of “subduing the inclination” itself comes from an inclination. One inclination subdues another.)

As for learning:
1. If what is hard is starting to learn, that is a matter of inclination, and it needs to be subdued because of the obligation to study.
2. If the topic itself is boring, then there is no issue of an inclination that needs to be subdued. Boredom is not an inclination but the absence of inclination, and in addition the learning will not be the best possible learning.
3. If the topic is interesting, then there is an inclination involved, the inclination of curiosity, and it is forbidden to subdue it, because there is an obligation to study.

The basis for the distinction is whether it helps achieve the goal of “subduing his inclination and correcting his attitudes.” Without learning there is no correction of understanding.

And therefore also regarding case 2: there are situations where even when the topic is boring, one still has to study it because it will later help with other learning.

I thought about this topic again recently, and in light of the Talmud in Pesachim 113b, which says:

“There are three whom the Holy One, blessed be He, hates: one who says one thing with his mouth and another in his heart; one who knows testimony in favor of his fellow and does not testify for him; and one who sees an indecent matter in his fellow and testifies against him alone. As in the case where Tuvia sinned and Zigud came alone and testified against him before Rav Pappa. Rav Pappa had Zigud flogged. He said to him: Tuvia sinned and Zigud gets flogged? He said to him: Yes, for it is written, ‘One witness shall not rise up against a man’ (Deuteronomy 19:15), and since you testified against him alone, you merely gave him a bad name. Rabbi Shmuel bar Rav Yitzchak said that Rav said: It is permitted to hate him, as it is said, ‘If you see the donkey of your enemy lying under its burden’ (Exodus 23:5). What enemy? If you say a gentile enemy — but wasn’t it taught that the ‘enemy’ they spoke of is a Jewish enemy, not a gentile enemy? Rather, obviously a Jewish enemy. But is it permitted to hate him? Isn’t it written, ‘You shall not hate your brother in your heart’ (Leviticus 19:17)? Rather, it must be a case where there are witnesses that he committed a prohibition — then everyone would also hate him. So what is different about this case? Is it not a case such as this, where he himself saw in him an indecent matter? Rav Nachman bar Yitzchak said: It is a commandment to hate him, as it is said, ‘The fear of the Lord is to hate evil’ (Proverbs 8:13).”

It seems there is no problem with the inclination of hatred itself, since it is ruled that it can be an inclination for the sake of a commandment. So I thought to distinguish between a situation where a person is entrenched in the inclination, like a person addicted to alcohol, in which case it is proper to subdue it, and a situation where a person is in a balanced state with respect to, say, the urge to drink wine, and still deprives himself of wine. For such a thing, he requires atonement.

Regarding subduing the inclination of hatred, several later and medieval authorities have already written about this and explained it in a number of ways. Some explained it similarly to your suggestion. I think Tosafot there and the book Tanya say something along these lines.
You are expanding this to all subduing of inclination, and explaining that it is negative only where the inclination does not rule over him, but rather he activates it according to his own decision. That sounds completely reasonable to me. Obviously there is no sense in eradicating inclinations. They were not created within us for nothing. What needs to be eradicated is the state described as: “the wicked are delivered into the hands of their inclination.”