The general idea was that people from Winhill knew about Squall's parents, and because of the family resemblance, realised that Squall must be Raine's son and therefore Laguna's. Squall and Laguna's relationship would've been pretty much an open secret, so that would've been easy to find out, and the boy from Winhill assumed (correctly) that only Laguna knew about the family resemblance, and so in a sort of loyalty to Raine/Winhill families, murdered Laguna because he was in a relationship with Squall knowing that they were related. :/