If possible you could try to 'turn off' DTR in your serial communications.. that'd doable...
the harder way, i havent even thought of before could be using a SoftSerial Library, attaching a com port to it and reading that one..
In the end the best way for you would be either to cut the pads (seems to be easy enough) and bridge them for uploading (as this is easier than the timing game) or get yourself a Seeeduino from nkcelectronics.com (which i would prefer!)
edit
Here they were talking about various ways of turning off autoreset as well:
http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1213719666/28