How much is too much - spokes protruding into the rim
That is poorly built and unacceptable (in my book) as a paid for product.  If all of the spokes are protruding some, and several more than others, it means that the wrong length spokes were used.  

The reasons for this may or may not be the wheelbuilders fault, it's possible that some component of the wheel build had incorrectly listed sizing and the spoke length calculation was off because of it (component manufacturer fault).   However, it's also possible that the wheel builder didn't have the proper size spokes.  The right way to do it in that case would be to take longer spokes and run them through a spoke cutter to get the proper length.  

In the first case, rather than rebuild the wheel the extra spoke should have been filed down to the level of the nipple.  This is acceptable as long as there is enough thread left to properly true the wheel.  If too much is sticking out the wheel will need to be rebuilt or it will likely fail at a future truing when the nipple no long has enough threading to secure purchase on the spoke.  

If the second case is true, and the builder doesn't have a spoke cutter and didn't want to order the proper size, I'm calling foul and would not send future business to them.

Unrelated to all that, it may be possible to get a rim strip thick enough to sufficiently protect your tube, but you really shouldn't have to go to that trouble.