I'm not really sure I'm familiar with the vac you are describing, "one like Cindy Bee used with the plastic bucket and the box top that comes off"...
That being said, I've used a bucket style vac with basically NO "bee Kill" issues. My configuration actually puts the bucket on it's side, arguably giving the bees more room to spread out and help reduce heating issues. However, I know a number of people that use the traditional style "upright" bucket vacs without issue.
I think the two points Robo mentions are quite important, as well as making sure that your suction is not at too high of a level.
These four basic rules have served me and my bucket vac quite well....
First, I keep the suction very low.
Second, I never leave the catch container in the vac without running the vac to keep the air flow moving.
Third, I put my catch container on the front seat with the A/C cranked for the ride home to keep them as cool as possible.
And forth....I get them hived ASAP!
I've done cutouts and swarm removals on 90°+ Louisiana days without ANY noticeable bee loss.