In fact, there is a global way to turn this behavior off in STELLA. Go into "File->Default Settings..." [or "Preferences..." on the Macintosh]. Choose the "Stock/Flow/Converter" tab from the pop-up menu at the top. Select "Biflow" under Flows and turn off the "Non-negative" checkbox under stocks. Press OK, and you will never have non-negative stocks or uniflows placed in your models again.
This capability has been in the software since around 1994.
We periodically toy with the idea of changing the default settings (as shipped) in the student version of iThink and all versions of STELLA to this set-up. The reason for this is that our business users (iThink) largely rely on the current constrained settings (indeed, this "misleading" feature was added at the request of business users who do not care for negative bank balances, for example, and do not wish to always add the first-order control required to constrain it).