Pulling the wire/s out of termination no.3 is ok (then compaire router stats before and after to confirm this has made a difference or cured a problem)
Cutting it back, err not a good idea. you might want to reuse this wire to either get the bell wire working again, a 2nd line running on the same cable, or as a tempory fix if one or both of the 2 & 5 wires goes faulty. Just tuck it back, although avoid coiling it, may look neat, but this can sometimes cause problems.
Remember without a microfilter in a socket then any equipment reliant on the bell wire will not ring on an incomming call on any extentions (only some, but by no means all moderm apperatus are able to ring without the bell wire) Also if you find (or someone who's moved into your old property) your phone dosn't work then a BT engineer comes out and "Here's the problem this wires disconnected" "Doh" particualy as this would be a chargeable visit.