I currently have 3 pregnant wolves, but I only have 2 spots for wolves left. They are also about 52 hours pregnant, so I fear I can't get rid of any wolves before then.

You can always free range your wolves, retire them or put them up for sale and advertise in sale chat

If you have at least 10 apples you can get 5 more spaces via

Marketplace>Barter>Apples>Den Expansion

This is why your better off keeping with the starter wolves and if you breed more than one that it don't fall in the same time as others