It is more in line with the existing story elements.
We see Gunray insisting on Padme's death as a precondition of his remaining in the Confederacy and Dooku trying to placate him (the story he falsely spins in the current version is to bide for time but it could be reworked so he is being sincere).
Dooku wants her alive to try and stop the clone army being deployed, Gunray wants revenge on the woman who got him kicked out of the Republic.
Basically Dooku is a good guy who has the Galaxy's best interests at heart but to do what he needs to do he has to work with despicable people.
As for the action elements it's actually more simple.
Why does a formidably armed bounty hunter get another formidably armed bounty hunter to kill a woman with poisoned bugs anyway?
If the idea was to hide the means of her death why blow up her ship in such an obvious fashion in the beginning of the film?
None of the assassination strands of the story make any sense at all.
It makes much more sense if the two bounty hunters are rivals and one kills the other leading not to Kamino, a mystery that leads to nowhere in the theatrical version but to Geonosis directly, which makes sense of the investigation plot strand.
If you have a robot assassin why have a non robotic agent at all unless to counter the previously seen unreliable nature of robots for this sort of work?
It's ability to melt glass is the very reason why I would cut the bugs and have it try to shoot her so basically it's a floating remote control gun and Zam is a snipper by proxy.
Even Sherlock Holmes has had plot lines like that.
It gives Zam something to do rather than just wait to be captured by the droid leading the Jedi to her. Get rid of the gun and replace it with a remote control device (it's straight out of an early Bond film and they are easy enough to follow).
Once captured she could mutter something about Geonosis and that could be the missing planet Obi-Wan investigates.