It goes like this. The Walders - or at least LW - were in the crypt. The Walders are among the very few familiar enough with Winterfell to know the location. LW was attacked by someone - or some thing - lurking in the crypts; or, alternatively, immediately upon leaving them.
It's possible, but he could be completely innocent. Likely suspects include Theon, Mance or his companions - known murders all, and the mysterious Lady Barbrey Dustin [or an agent of hers,] all of whom have knowledge of and/or interest in the crypts, and a variety of motivations. I'm leaning toward Mance, a man of many secrets, who I suspect to be lurking in the crypts.
UPDATE [10/1/16]: While the other murders at Winterfell were certainly committed by the Mance crew, Little Walder was definitely not their victim. My bad.
As an afterthought - BW is not stupid. Were he the actual murderer, there would have been some attempt to cover his tracks - or, in this case, spatters. There was none. Anyone who has ever read a mystery novel should be looking in a different direction for the actual culprit.
As a second afterthought, it's widely accepted that in some way the crypts are going to play an important role in the ensuing events. Leaning toward the crypts and what may be lurking there rather than Big Walder simply makes more narrative sense.
As a third afterthought, there could be some wild beast in the crypts. There's speculation of many things down there: Rhaegar's harp, the true Lightbringer, a dragon's egg. More remotely - we have no recent knowledge of Nymeria. Could Arya's lost dire wolf have made it's way down there? Is there a secret entrance outside the walls? None of this would surprise me, and Nymeria will almost certainly have a role to play before its all over.
Last afterthought - the thought processes involved in writing this have convinced me that Big Walder is, in fact, NOT the murderer of Little Walder.