There are risks when you run JetStress where Exchange is installed.

There are two primary risks associated with running Jetstress on a machine with Exchange installed. The first has already been discussed (Jetstress could potentially delete some existing logfiles if it's configured to use the same log drives that Exchange is using). The second is that if you use a version of Jet (ese.dll and eseperf.*) that is different than the version installed with Exchange, you'll end up registering the Jet database counters in the Jetstress install directory which will cause the database counters for Exchange to be broken after Jetstress is removed. That can be solved pretty easily by running the following two commands from the Exchange bin directory:

unlodctr ESE

lodctr eseperf.ini

Having said all of that, we still recommend never running any of our pre-production test tools on a server that has been deployed in production.