I know about 3 guys named
Tim, but I've never heard any of them called
Timothy once. They get called
Timmy every once and a while as a joke but none of them ever get called
Timothy. It's one of those names that most people assume if someone's name is
Timothy, they go by
Tim.
IMO, if you don't like the nickname, don't use the name, especially with boys, because boys as so much more likely to use nicknames.