In my experience, you are over thinking this and going towards a worst case scenario that is not likely. It is, however, good to verify.
I went to a university that not only offered, but required internship credits for their engineering degrees, and the work was always compensated. Companies that advertised through the university knew the deal and were prepared for it. For a company, working with a university to get interns means you usually get a really good sense of what the interns can do, and you get input into helping the educational program so that each year the interns actually get better. In return the college expects the company to do some paperwork and provide feedback to the university in a particular format that can be used by both the school and the student for self-improvement.
If you are working with a company that you connected to through your school, it doesn't hurt to verify - call your recruitment contact and make sure that they are aware you want to do the internship for a college credit.
If you are working with a place that you found without working with your school, and you want credit for it in the university, you may need to be prepared to do some administrative work.
- Talk to your school and find out what the process is for you to get credit. Make sure you know what the employer has to do.
- Schedule a talk with the employer so you can discuss the needs for the credit program. Have the paperwork they need to do ready and figure out with them who can do the paperwork. Do this before you show up on site that first day and make sure you have names and dates planned with them, so that everything happens on time.
- Manage the dates. Make sure the employer doesn't forget and verify with the school that the papers are complete.