Stealth v Perception checks are an issue. I have rolled in secret for this kind of stuff before, although I don't like it.
One way round it is what I call the deferred conflict. There's a magical silent alarm at the doorway to the temple, which if triggered means a guardian spirit is now waiting for them in the main hall. Did the players trigger it or not? Well, if it's a silent alarm, and so they wouldn't know they triggered it, you can make the Stealth check after the fact, when they enter the main hall. 'Guys, there was a magical silent alarm back there, make a Stealth check'.