Is there a way to tell the AH not to take Gems into account when searching?
Solution 1:
As of 1.0.4, searches do not take into account gems when searching, so you don't need to do anything special.
Solution 2:
Short answer: NO.
For now the search in auction house is still unsatisfactory.
Search could be better, there is no way to search for DPS on weapons.
Some searches generate no results bug when you switch the order of buyout for example.
Lets hope they fix the bugs and improve the AH asap.