Think the Anakin jump removal is almost frame-for-frame what I did in my cut... great minds think alike old chap :-D
You're on the right track with how to remove Yoda but I think in order for it to fully work you need to:
A: Give Dooku a reason to leave and not to just kill them (The original reason is he can't defeat Yoda)
B: Change Dooku's emotional reaction at the end (The original has him giving a blank stare, which is fine for a mid-sequence shot... not for the climax)
If you could show Dooku leaving as a result of Padme and the Troopers arrival that would give Dooku a natural reason to flee (You partially implied it I know) and as an added bonus it would mean Padme saved the day. You could have Padme arrive, then cut to her running inside (You'd have to erase Yoda from that shot) and add the troopers firing and shouting etc, then cut to the shot of Dooku running up the ramp, then we see his ship blasting out of there.
Could you change the Dooku's reaction from the sigh to a more gloating feel, a smile would do.
Or recut it so Dooku could start to pull the ceiling down onto Ani and Obi and Padme gets there in the nick of time and he has to flee.
Or recut it so he stats to pull the ceiling down onto Anikin and Obi, when suddenly Yoda appears saying "Dooku!" and they have the force battle of strength before Dooku brings that column down and runs why Yoda is busy.
This could work nicely as it would mean Yoda was arriving at the last possible second to save our heroes from Dooku killing them.