The system.js functions are available to Map Reduce jobs by default ( https://jira.mongodb.org/browse/SERVER-8632 notes a slight glitch to that in 2.4.0rc ).
They are not actually eval
ed within the native V8/Spidermonkey evironment so tehcnically that part of them is also gone.
So no, there is no real problems, they will run as though native within that Map Reduce and should run just as fast and "good" as any other javascript you write. In fact the system.js
collection is more designed to house code for map reduce jobs, it is later uses that sees it used as a hack for "stored procedures".