As far I know it was not his alleged Germanophilia (or Prussophilia) the main reason he spared Prussia of its imminent defeat, but more like he wanted Prussia's help into his inevitable war with Denmark for his family lands. He, as the Duchy of Holstein, wanted to gain the rest of the Danish controlled regions in the duchy, and for that he needed all the help he could get, Prussia being the most logical option as they were the powerhouse of the region.
If Prussia fade into irrelevance after the Seven Years' War, I don't really know what would be his next options. Maybe Sweden? The problem with Sweden was, as far I know, that they also claimed part of that duchy, so he would have to make a deal with them, thing that I don't know if Peter really wanted. Probably would defeat the purpose of getting their help, in first place. Or maybe he goes alone in his adventure, but that would also risk into angering the Russians for going into a war with little gain for them.
What happens then, who knows? I don't know what his next steps would be to expand the empire, if he expands it, at all. Maybe he would calm a bit and start to defend and develop what he had, building an alternate Kiel Canal to avoid having to pay the Danes the "Sound Dues" aka the toll fee of the Danish straits, for example.
Keeping Prussia and wanting to annex Courland after it would be "wanting the cake and eating it", and probably would worry the Polish nobility too much they would be motivated to ask help from other neighbors to counterbalance the Russian expansionism in the region.
Besides once Peter ascends to the throne, he probably would give back the duchy to the Hohenzollerns, anyway. So probably doing the Prussia-Courland change probably would be the best thing Elizabeth could do before dying.