Yeah, A good spy can take out an entrenched engineer and can be quite annoying. I have yet to really find a place on any map that it is impossible to remove an engineer and that includes custom maps. I have played on custom maps that are really easy for an engineer where I have been able to sit in one location for most of the game, but the thing is once the other team learns the map they start to coordinate themselves.
As for spy backstabs they are unbalanced right now and in my opinion buggy in the favor of spies. I have lost count of the number of times I have been "backstabbed" in the side, where they are not behind me but still get a backstab kill.
I am more worried about spys than ubers. The only real uber I am afraid of is an Uber Pyro. An uber heavy is a joke if I am hiding behind my sentry, I can repair it faster than you can kill it, uber demo man is only a danger if they use their stickies which 90% of them dont do, or dont do fast enough, uber soldiers tend to only get off a couple rounds that hit me so I do alright against them. But Uber Pyros are scary, they can run up and toast me + sentry gun at the same time and do it fast.
A spy + pyro is crazy scary, I will be running around repairing my sentry and wacking the spy with my wrench and then the pyro comes running in and toasts me.
Overall I see the engineer as a delaying tactic, because at this point after the release of TF2 most people have figured out how to get around sentry guns but it just takes them a little bit to accomplish that.
As for a lone pyro vs. Sentry gun that only works if the engineer is not really smart and places the turret to close to an entrance.
Overall I think the worst enemy of a sentry gun is its range. Most custom mappers think an easy way to put a check against a sentry gun is to make the strong points in their maps have entrances just out of reach of the ideal sentry placement. This is annoying because then the sentry guns are essentially useless there. Its not that hard for a simple combination of enemy forces to really crush an unsupported sentry gun as it is and to throw the range card at it is just not fair.