If you are not actually going to leave a jack I would suggest actually disconnecting the wire at the other end completely and label it. So if you do want to use it in the future you will know whats what. Leaving a live phone wire stuffed in the wall is not really a good idea. If you really have to leave it live, make sure that all the conductors are isolated and well wrapped up with electrical tape. Just chopping the wire and leaving it may lead to line noise down the road - which may be hard to find if that live wire without a jack is forgotten.
Also do not chop it off short, that makes the wire unusable for anything else ever. Undo the connections or cut them just shy of the screw terminals.
Another good alternative would be to get a multi-port wall plate with insert jacks. These allow you to mix phone and network (and other stuff) on a single plate. So you can keep the phone jack(s) and just add the network jack. The connections are all punch down type 110 and easy to do, I think the retail packs include a mini punch tool.
Home depot has these in the phone/network section,
Wall plates,
http://www.leviton.com/OA_HTML/ibeCCtpSctDspRte.jsp?section=10422&minisite=10027 Jack inserts,
http://www.leviton.com/OA_HTML/ibeCCtpSctDspRte.jsp?section=10231&minisite=10027Cat3 jacks are for phone.
