Yes, the recess appointment of John Bolton is constitutionally troublesome

Which isn't the same thing as saying that it's unconstitutional. President Bush is, in fact, obeying the "letter" of the Constitution by appointing Bolton while the Senate is in recess:

The President shall have Power to fill up all Vacancies that may happen during the Recess of the Senate, by granting Commissions which shall expire at the End of their next Session.

While the move isn't unconstitutional, it is troublesome, since this clause was clearly meant to provide for the occasion when a post becomes vacant while the Senate is in recess, and there is an urgent need for the post to be filled before the Senate reconvenes. This was a relevant issue when the Senate took long recesses, but now it's anachronistic.

But what other choice does the president have when a nominee has majority support in the Senate, but the minority refuses to allow a vote?

The recess appointment controversy would go away if, as James Taranto suggested, the Senate was compelled to vote on a nominee within 90 days of the nominee's name being submitted.