I think you're on the right track, but it depends on how soon the ground level is raised. If you really do it within two years, you're probably OK, but if you wait longer, the trees will have roots spread far and wide (especially if they're by a lawn, which will provide ample water for root growth). The problem then is that covering the roots with a bunch of new dirt will likely suffocate them. If it were just a few inches of dirt, it would probably be OK, but more than that will cause problems.

I think the best solution would be to just plant them how you want them and then when the basement is dug, have the excavated dirt hauled away. You may find uses for some of it around the yard without a general raising of the ground level -- maybe a few berms here and there.

This is coming late- but could you build a big berm to plant the trees in now, and then when you raise the soil level, the trees will already be up higher.

We have really heavy clay soil, so we planted our fruit trees in a berm to allow better drainage.