You have to use another SCV.
That you do is factored into the balance of the game. For gosh sakes man, you have mules, it's enough money.
Edit: I believe Mark's answer is wrong. There's no way to prevent a scouting worker from seeing your build with a SCV and that has nothing to with whether or not you should use a second SCV.
A long time ago I wrote about scouting, and I really think it'd help you to go back and take another look.
The purpose of scouting is not omniscience. Getting that level of scouting would cost too much time and effort and just wouldn't pay off. Instead, scouting is largely to get an idea of what they're doing at the current moment.
You don't need to know every time they build a Starport, or take a new Expansion. You don't have to be on the ball with your army half way there to counter whatever crazy tech switch they're about to pull, if that were the case this game would be all about deception and hiding your next building.
Keep this in mind when you're considering the following.
The number one way people scout is skirmishes. This may seem like a strange concept as it makes sense to want to know what your opponent has before engaging them, but usually the way player figure it out is those quick little back-and-forths in the middle of the map, or the drop in the back of the base, or a fly by with a group of Mutalisks.
The reason these are so telling is they give you an idea of what he has right now, and where he's going. Notice he added on a couple Vikings since your last fly by? Maybe you see a Colossus laser eat your dropping Marines. Personally, I always find Thor missiles to be a good indicator that he has Thors... and probably more coming.
With the exception of maybe some Dark Templar rush or Hidden Void Rays there isn't a lot your opponent can build up in secret that will make a huge difference; and for those sometimes cheesy plays, there is no cheese that can't be handled by standard play. Unless you're going for some crazy Cheese yourself you should be in a good place.
So my advice to you: Stop worrying so much a live a little. Sure maybe when you suicide a Marine for intel he doesn't see a Carrier, but you know what? Unless you're doing something crazy, that's ok. You'll catch them before he has more that 2-3.
Alright Tzenes, if trick plays aren't some unmanagable thing, why am I Scouting?
Scouting is supposed to give you a feel for what your opponent has. Its supposed to give you answer like: BioMech on 3 Bases. Its not for things like: OMG he built a tech lab on his second Starport! Starcraft isn't precise enough a game yet that you can know exactly what that means and how to counter it. Maybe for the first 3-4 minutes of the game, but after that point you just need a general feel.
No Zerg player can go Muta/Infestor/Broodlord/Ultralisk in a undecided game, so chances are if he's producing one of these you probably know what to expect and where he can go next.
Best Answer
Given the attack target priority, a unit will attack units over the barracks. Overlords tie with other hostile units, so they are treated equally. In your Zerg example, there's nothing that would tell the AI to favor other zerg units as opposed to overlords except the player's micro.
In terms of the Terran example, the units should favor the opponent's hostile units over the barracks. What may have been happening is that, given nothing else in range, they continued to attack the barracks. In this case, moving the stalkers so that they are in range of units with higher attack priorities should cause them to favor the opposing army over the barracks in the sky.