I don't think you can specify which server it gets started on, but you may be able to just stop it later.
But first, a front-end server is a front-end server because it has the "Microsoft SharePoint Foundation Web Application" service started. So, disabling it means its no longer a front-end server.
Anyway, here's one approach. Towards the bottom of your Input XML file, add a new node, like so (I put this after the <Forefront> node:
<NoSPWebService Provision = "SP_App1, SP_App2">
Then edit the AutoSPInstallerFunctionsCustom.ps1 file and put in something like this:
#Region Remove SPWebService
# FUNC: Remove SPWebService
# DESC: Removes the SPWebService on specified servers
If (ShouldIProvision($xmlinput.Configuration.NoSPWebService) -eq $true)
You have to reference this "RemoveSPWebService" you just created, so I recommed editing AutoSPInstallerMain.ps1 and putting that in right after "InstallForeFront $xmlinput"
Just type in "RemoveSPWebService $xmlinput" on a new line. That should do it, I haven't tested this and its just one approach. I've never used the "StopFoundationWebService" function, but it exists in the latest version.