That's the nature of the beast! It all depends on where you place your guards and where the objective is hidden (remember to use blinds). It's up to the attacker not to trip the alarm and guess where the objective is, otherwise all hell breaks loose before it can be achieved. Also remember to roll for reinforcements for the defender at the end of every turn. The point of the stealth mission is to develop a sense of tension.
Glad to hear you're enjoying the conventional game too.
One tip I'd suggest. You don't use elite troops to guard supply dumps. That's what your REMFs are for, so take a defending force of professionals or conscripts. Mind you we've played Militia attacking a Contractor compound, that was an enjoyable game too.
Guy