If I understand your question correctly, you have lined up an internship with Company A and a job with Company B. Company B is cool with the internship. Company A are likely to ask you to apply for a full time job.

You want to work for Company B and not Company A, but Company A would also like you to work for them.

My advice: Work for Company B. It's where your passion lies, it sounds like it's a rare opportunity, and the pay is better. The downside is you will mildly inconvenience Company A, which might make it tricky to go back in the future, but honestly, if they pay low and you're not that interested, should that really be an issue?

It reflects well on your personality that you feel bad for inconveniencing the recruiter, but you won't be the first one, or the last.

When it comes to this sort of thing, you have to think about what **you** want most. If you join Company A out of guilt, you'll regret your choice of joining Company B and will more than likely grow to resent your job, at which point you'll probably end up quitting anyway!