A Tower Controller reported they had to vector an IFR helicopter that departed from a nearby hospital below the minimum vectoring altitude to avoid conflicting traffic.

Narrative

I was working local/ground/clearance/flight data combined with a stand-alone CIC (Controller in Charge) in the tower cab. Helicopter landed at ZZZ hospital. After they completed whatever business they had there they called ZZZ clearance for their IFR clearance to ZZZ1. ZZZ is an uncontrolled helipad at one of the local hospitals.I was unsure what exactly this meant for me when they called up ready for departure. I got confirmation they would maintain their own terrain obstruction until 2200 MSL because that is our MVA. I told them departure would be at their own risk. On departure before they got to 2200 MSL I had to vector them from their direct; approximate heading 158; to a heading of 180 for incoming traffic to Runway XX. They were at approximately 1200 MSL when they were vectored. There was no loss of separation between the incoming aircraft and the helicopter. I was uncomfortable with a helicopter departing the hospital's helipad as IFR. That seems to be more of an approach control function more than a tower function. I have never seen this; and the CIC in the back said he has never seen this situation before either. Suggestion: I have no recommendations from this event. This is a rare scenario that I; nor the CIC had ever seen before. After talking to the CIC in the back there were other avenues I could have taken; such as departing the helicopter VFR and giving him the IFR clearance in the air.