I stopped using the Gmail app and started using K9 mail, mostly because I have several email addresses and not all of them are Gmail accounts. Within the settings of K9 there is an option to delete messages from server when deleted on phone and it works the other way around too. so it you delete message from the web it should delete them from the phone too. I haven't looked but I would guess that there is a similar setting in Gmail that would do the same thing. If not switch to K9 and you will be all set.