I haven't tested this in particular, however:
Stopping a transaction in progress, in itself, will not necessarily cause problems and it will rollback - any sort of transaction, including replicated transactions on on a Subscriber from a Publisher. This is because of the ACID properties that always apply to transactions, specifically, the A being Atomicity - either everything in a transaction occurs, or nothing occurs. So a stopped or failed transaction will be totally rolled-back.
I don't know of any other way to stop the transaction being replicated, however use sp_setsubscriptionxactseqno
with caution, not only do you need to be sure you get the LSN correct but whatever happens it'll mean you're Publisher and Subscriber are no longer truly in-sync. In practise this might not matter, but it should be a consideration.
If you haven't already have a look at Technet / MSDN (more or less the same article depends whether you prefer Tnet of devNet), if you haven't already, and this blog post on MSDN, that'll help.
N.B. sp_setsubscriptionxactseqno
needs to be run on the Subscriber (and each one on which you want it to skip).
The alternative, and with no other information, what I'd recommend is just let it run. It might not be ideal, but it's the safest and least work. Is the system that mission-critical and time-dependant that the 2 days will cause significant problems?
Finally, as general advice if you're not sure what to do - fob the decision off to your manager or other higher ups. Present the options, work involved and risks/impact (including the option of just doing nothing), and blame (subtly and office-politically-appropriate) the person who made the initial 'accident' (unless that's you, then maybe you don't want to tell the higher ups).