What does your CA PPM implementation partner recommend to fulfill your requirement? Just curious as I know you stated "We've been informed by our implementation partner that there is no bulk upload / enable capability and no way to run a script and upload a file of the employee id's to enable", surely they have proposed something.
Might there ever be the time where a contract that is disabled needs to be enabled for time entry? Especially if the contract is changed via CR at a later date?
Might there be an occasion where the same vendor has multiple contracts, and some resources can span contracts? For instance an architect is on Contract A - time entry for 50% of his/her time and on Contract B - no time entry for the other 50%. So, then you have to look at enabling and disabling the Open for Time Entry for the resource at the project level. Would you allow an override? Does there need to be process that enforces the settings, in the event that a PM or Admin changes the Open for Time Entry attribute?
Time tracking can get quite interesting once complex requirements come into play.
Which version of CA PPM or you deploying? Hosted, On Premise, SaaS?
Depending on your complete requirements I can see XOG, custom objects, possible custom processes, GEL, etc. However, it is always fun!