I would also like to see the exclusion filters apply to the Threat Target File Path field. This seems like the most obvious way to combat the problem.
The suggestions to use high/low risk processes rules unfortunately have no bearing on the Access Control policies.
While HIPS policies may give you finer control here, HIPS is a complicated beast to deploy. This should be a simple thing. If you have a rule that is described as "controlling scripts" in the temp folder, and you have a provision for exclusions, then the exclusion should at least apply to the script name and not the interpeter. This is a good idea but unfortunately the implementation renders useless.