They didn't know precisely how the Stone retrieving would go; this is evidenced by War Machine expecting spears to rise from the ground, à la Indiana Jones, when entering the temple. Nebula might have known a bit more, having spent some time with Quill since GOTG2, but she didn't seem to have much more info either.
What they knew, on the other hand, is that there was a possibility of Peter Quill incoming1. He would not have been expecting to find anyone on the planet, and things could have gone very awry, very fast.
By waiting a bit more and knocking him out, they were ensuring their retrieval of the Power Stone wouldn't be jeopardized.
1 Memory says some door was closed, meaning he hadn't entered yet, but I'll have to check that.