I've had my starters overflow many times and have not had issues with infected yeast. It sucks to see all the good yeast go to waste, however. I now do starters in two containers:
1) 2000ml flask
2) 3gal (~11000ml) bucket
In the flask, I won't put more than 1500ml wort/yeast (the flask is probably ~2200ml).
In the bucket, I do 6000ml starters.
Neither of these overflow with those volumes.