I work and bike alot in milton, and while there are certain roads i would avoid, i wouldnt avoid the town all together for that reason. For the most part i would stay off Derry Rd, especially in the new contruction area between 6th and 1st line.

It might be easier to give you the route i would take into milton (actually i am thinking about commuting a few times a week from mississauga).

URL for this route is: http://www.gmap-pedometer.com/?r=236901

Basically the route is layed out from Trafalgar and Lakeshore in Oakville, head north over the qew, over to 6th line on a residential street, then up 6th to 5th, up 5th to mainstreet.

Of course once in milton getting over to Kitchener has lots of options, lots of rural roads, and of course a steep long climb up the escarpment. another option is to take britannia from 5th line and then heading towards kitchener on side roads.