Broken off flush?
There really isn't a whole lot of good options for a steel screw broken off in an aluminum housing.
Whatever you elect to do be sure to keep the inside of the pump operating room clean.
Pump removal and replacement of the housing by an injection pump shop is an option. Could also buy a rebuilt pump outright.
After sealing up the housing with lint free rags and a bunch of duct tape I would be inclined to slather the broken off screws with a good penetrating oil for a day. Maybe tap the threaded housing bosses lightly on the side with a small hammer. Measure the one fastener you were able to remove. Look up the minor diameter of that screw. Buy a left handed drill bit slightly smaller than the minor diameter. Center punch the broken fasteners, then drill them out with the left hand drill. With any luck that will extract the broken screws. If not you will need to get your hands on a correct size screw extractor and give that a try. If that does not work your last option if the bosses are large enough in diameter to Helicoil them. Purchase a Helicoil kit for the size fastener it uses, then drill, tap, and insert helicoil with tool.
All the stuff you need can be purchased from several sources including McMaster-Carr