First, God bless you for going into general surgery... I think that is one of the toughest fields out there.
Second, Dean's are typically right about most things... so if they say submit, then consider it.
The bottom line is that your application from a surgery standpoint sounds great - letters, the rotation, etc.
Your other grades are around HP/P... that's fine.
According to various posts, programs can filter Step scores (they can set a filter for just Step 1, both Step 1 and Step 2, or screen however they please). That being said, there are a few outcomes here.
A. Rejection or screened out secondary to Step 1 score
B. Program will wait for Step 2 score to see if improvement
C. Other scenarios
Please consult page 92 of this document:
http://www.nrmp.org/data/chartingoutcomes2009v3.pdf
The subsequent next few pages contain the Step 2 data as well.
Best wishes.