Worrying about spambots and trolls is basically a premature optimization. You call this a niche site but some how it is going to be popular enough spambots and trolls will want to come. If it is truly a niche site then popularity will by definition be limited. So which is it, niche or hugely popular?

Even if it is a non-niche site, your assuming it will be popular with trolls/spambots. So as you can see your worrying about a problem you may never have. However, you are wise to think about it and be ready.

Since you said you want this to be a learning experience, go ahead and write your own commenting system. It will teach you a lot. Put up some small barriers to prevent spam. Captcha, email verification, SMS verification, etc. These are all pretty easy to do and there are services that will help you out.

Lastly, if it does become a troll hole then be prepared to migrate your data. I would say put off writing any migration scripts, but maybe look at the comment services and see how you can import comments. I've done this before on Disqus and it is not too hard.