I don’t see anything explicit in the rules that prevent a negative score if penalties exceed goals. I suspect this isn’t intended and the lowest possible score is zero.
A particularly interesting consequence is in the area of seeding points. If an alliance is being badly beaten, and has given up hope of taking the lead, it my intentionally incur penalties, which will result in a lowering of the winning alliances score when the coopertition bonus is added (or rather subtracted!) due to the negative score.
I would have to think this was overlooked by the GDC.