Yes you can. The two guards are treated separately.
My wife and I played last night (friends in our board games club gave me Ninjato for my 30th birthday!) and the following scenario came up:
My wife called out 'Banzai' on a red treasure knowing that she would have to face an Elite guard (or maybe two Elite guards) and as fate would have it the Gijon/Samurai two-guard Elite was pulled. In her artillery she had two Dojo cards (a 3 and a 5) and the Seishin-teki Harmony card, allowing her the ability to switch from Stealth to Strength. At that point she was in Stealth mode.
As Gijon is a 3 guard and Samurai a 5 guard, it means she would have lost against both provided she faced them in order (from left to right). However, she asked whether it is allowed to first face Samurai with her 3 Dojo card, switch to Strength using the Seishin-teki Harmony card and then face Gijon with her 5 Dojo card, thereby beating both guards. Being the perfect gentleman I allowed it (although it ultimately cost me the game - I lost with 4 honour).
So Adam, my question is, in the future (especially when our friends are joining us), is it allowed to face the two-guard Elite in any order as we did or not?