Alistair,
I have not had a specific water pump problem, such as you describe, but of course the same difficulty arises where any steel stud passes through alloy. In the Weller engine the scariest example is found with the head mounting studs in the block.
For what my tuppence ha'penny is worth here are some suggestions:
1) In this application penetrating oil doesn't penetrate. Degrease and then use Phosphoric Acid and water 50/50. Coca Cola works nearly as well, which might give you a clue as to whether or not to put it in your body. For best results you need to get the area immersed. Not easy, but I have built small baths out of Plasticine to keep studs soaking.
2) Heat is a great help, but there is such a large heat sink around in the form of the block that gentle heat is a waste of time. The trick is to get the steel stud really hot without damaging the alloy: Put sacrificial nuts on the end of the studs. Do not take them right down against the alloy. Heat the nuts to red hot with a very narrow flame, being cautious not to damage the alloy. I doubt any thing less than oxy acetylene will achieve this because of the heat sink effect. Keep the nuts red hot for several minutes to allow the heat to work its way down the stud.
3) Now apply a steady pressure behind the pump housing with a suitable bar. Do not be a gorilla, the alloy can be cracked. Whilst applying the leverage take a hard mallet and give the sacrificial nuts a smart blow in the opposite direction to your leverage.
If you have no joy at this stage apply as much profanity as you can think of and then repeat steps 2) and 3)
If by the end of the day there is still no result go and sleep on the problem leaving step 1) in place. Refreshed and renewed in the morn carry out step 2) and 3) again.
This sequence can be repeated until you succeed or until you lose your rag completely and drill the studs out. You will also be in a position to get some stainless steel or manganese bronze studs made so that the problem cannot arise again.
You will succeed.