Currently there isn't any built in method to throttle the download of patch files within Protect. Here are a few suggestions, though:
1) Submit a feature request at http://shavlik.featureidea.com. This will go to our product management team for review.
2) You could look into setting up scheduled scans with autodeploy to run after regular business hours.
3) I am guessing that the actual download isn't the only problem, but also the copying of the files to each of the target systems. It would help to look into using a distribution server for deployment. You can find more info on using a distribution server within Protect's help files. These would be good ones to start with:
Help > Contents > Common Tasks > Configuring Program Operations > Using Distribution Servers > Why Use a Distribution Server?
Help > Contents > Common Tasks > Configuring Program Operations > Using Distribution Servers > Configuring Distribution Servers
I hope that helps you out.