Yes, the pump has to come off to get the driveshaft out.
The pump should not be "Glued" onto the ski... but some people do, if they are too lazy to buy the proper seal. Seadoo makes a foam gasket, and the only place you need any sealant is around the water feed pipe.
One word of advice.... take the clip off of the driveshaft, behind the stainless ring before you remove the pump. You need the pump there to push against, to get the stainless ring to slide. Once it's off... the shaft will pull out, after the pump is removed.