I think they could have pulled this off, but not used the Yoda baby thing. That, in my opinion, would have seemed way out of place.
To me I think it would have been nicer to see Obi Wan and Yoda sneak into the Temple and not see any Clones at first. But then to see several "Jedi" from a distance, and for Yoda to sense something was wrong. Then it is revealed that there are Clones disguised as Jedi. Maybe just a few of them, not a big army or anything.
After killing them, I think it would have been very cool to see Obi Wan and Yoda in a scene in the temple reminiscent of ANH where the Stormtroopers blow open the door in the Death Star to get to the detention block where Han yells "Get behind me, get behind me" - maybe if Obi Wan yells "Get behind me" there it would have shown a lot more tension in the temple rather than just seeing a holographic effect of the slaughter and the 501st Clones getting killed.
Have them survive the onslaught of troops, change the beacon distress signal, etc. and then go off to face the Sith.