If I delete a file that has a trojan McAfee found is the trojan gone along with the file?

generally yes, unless it duplicated or installed itself somewhere else..but most times, its gone with the file

If I delete a file that has a trojan McAfee found is the trojan gone along with the file?virus removal

Yes it is, but you have to scan all your files, just in case the virus attacks more than one file

If I delete a file that has a trojan McAfee found is the trojan gone along with the file?anti virus protection

Turn OFF your sys restore points, del. file(could be in more plases then you realize, cross your fingers %26 reboot then turn ON sys. restore again. Most headaches back themselfs up in restore points.
yes but some of its files will be hiding