You can't be penalised according to the rules. You can't get an excess from machines. You can ask at the ticket office if you have time, but knowing SWT ticket offices the queues will be horrendous. The fare is the same on board as it is from the ticket office, they can't charge extra (if they did, obtain an unpaid fare notice, let us know and we'll appeal it and the guard will hopefully be given suitable training).
I think you are asking to travel via Leatherhead to London Road (Guildford) [LRD], then travel from LRD to Guildford, then on to Clapham via Woking? If so you can simply buy a ticket to LRD, which is the same fare.
Alternatively, yes a ticket to Guildford is valid for a break of journey at LRD. You could then resume your outward journey later, to Guildford. Then you'd start your return journey.