The ads in the installer, they don't hurt anyone, they don't hinder usage and you get a few bucks out of it, so why not??
I really like Sigil, and I don't want to see it go away any time soon; AFAIK it's the only one of its kind (in the Linux universe at least).
The point it, a developer working on an open source application must have a motive, as you said he wants an app to do a certain job that no other app out there does (or does finely enough), he gets a kick out of developing it... etc; in your case you were even lucky enough to mix your hobby with your studies, by making your thesis about Sigil. So yeah, if those ads aren't going to be too much in the way, I say all the better for you; Sigil deserves much more than the few nickels and dimes those ads will get you :)
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