jaazzzw

CPT is the way to go. However, CPT does not necessarily affect OPT. A friend of mine had similar opportunity and the response she got from the ISO is and I quote "Students who have completed 12 or more months of full-time CPT are ineligible for OPT.  Part-time CPT or CPT which totals less than 12 months does not affect OPT." CPT is much simpler than OPT and do not require an EAD card (I interned at a national company and I-20 with CPT is all they need). However, her school might have concerns about working on an internship while being a full time student, but that really depends on the school. 

Can you get an appointment at USCIS to ask them about this? It seems too complicated and I am not sure someone on VJ will know about this.
 
https://my.uscis.gov/appointment
 
You can do an appointment to submit an application in person and take the paperwork filled out. If there is something you are not sure with, you can leave it blank and ask them.
 
Anyway, that is what I'd do if I were in your situation.
 
You should file a complaint with the university, maybe the graduate student provost or something, about what the office for international students did. It is unacceptable. It could have jeopardized your status and the fee is very costly.