I am a bit confused, why would your company not want to process your clearance? It should not have any affect on your clearance once you get on active duty.
You are correct in that while you have completed your TS background investigation, you technically don't have a clearance until you are in a position that requires one. However, you are eligible for one that your current company would submit you for. Once that is done, you'll "read in" for the clearances you need and once approved, you should be G2G.
Feel free to PM me if you want to discuss offline. Don't bother with your ROTC det as they simply help you complete the necessary paperwork. Your company security officer or SSO would be your best point of contact.
Cheers! M2