Yes, coming out of limbo is indeed difficult.
It is made quite clear that being stuck in limbo makes you easily forget what is reality and if you stay for too long, you basically loose your mind in there. So just entering it doesn't already come without dangers, let alone finding and bringing back someone from there.
Ariadne: And if he dies?
Cobb: Worst case scenario, when he wakes up his mind is completely numb.
Saito: Cobb...I still honor the arrangement.
Cobb: I appreciate that Saito, but when you wake up you won't even remember that we had an arrangement. Limbo's gonna become your
reality, you're gonna be lost down there so long that you're gonna
become an old man...
It wasn't just about killing Saito in limbo, but more about convincing him to accept reality again, the shooting (which Saito then did himself) was just the expression and fulfillment of this will to exit limbo. But I admit that with Fischer it was a bit different (which isn't yet entirely understood, though). But maybe just dropping him worked for Fischer because he wasn't there for too long and not already an "old man full of regret" who abandoned reality.
And at the end we see from Cobb's weary appearance that it took him quite some time and effort to even find Saito there, let alone convince him of reality. And not even that, from Cobb's dull and glass-eyed gaze and his slightly hesitant and absent behaviour during his conversation with Saito we also see that Cobb is himself on the verge of forgetting this "truth" he came to remind Saito of, I think. And that is ignoring Mal, who was at that point also still around there (and who knows if Cobb hadn't lost himself with her if Ariadne hadn't called him to reason).
It thus certainly wasn't an easy undertaking at all to find and save Saito from limbo, even if successful in the end. So if you have the chance to avoid that and succeed with the operation before Saito dies, that seems the far less risky alternative, especially since "down to the lower levels the pain will be less intense", as we could see from the to a large degree fully functional Saito on the deeper levels (until it got too much, but they could as well have already been done at this point).
In addition to that the whole procedure of saving Fischer wasn't a proved piece of cake either. This whole idea seemed largely improvisation on Ariadne's side and nobody, not even Cobb, seems to have been in such a situation before. So they weren't entirely sure if it works at all. They also had their difficulties and it took Cobb some effort to finally get over Mal. But in contrast to Saito's injury earlier this really was their last resort now, there wasn't any way to complete the task other than trying to bring back Fischer by any means necessary. Hadn't Fischer been killed and Saito stood a little longer it wouldn't need to have come so far at all. But don't let the fact that it worked in the end deceive you into thinking it was just a walk in the park.