You're correct. If you do a staggered patch deployment (test computers THEN production computers, for example) you will likely run into this issue with the monthly IE cumulative updates, Flash Player updates, etc.
This remains an issue in 7.5 and the only way around it at this time it to disable the option to automatically supersede updates.
I have raised this as an issue with the product management team and I'll forward your comments to them as well.