weak top 2 pair on flop (limit crazy pineapple)

[gloyner 0]

Hero posts Big Blind with 9:spade: 7:spade: 4:club:4 calls, 2 folds, 2 calls, SB completes, hero checks.(8SB) Flop is 9:club: 4:spade: 3:spade:SB bets, hero calls, 2 folds, 2 calls, 1 fold, 1 call.Hero discards 7:spade:Turn is J:diamond:(6.5BB) SB checks, hero bets, 1 call, 1 fold, 2 calls.River is 5:spade:(10.5BB)SB checks, hero checks, villain bets, 2 folds, hero... reluctantly calls.Comments - discarded the flush draw, as thought it wasn't high enough... is that correct to keep a weak top 2 pair?Should I have raised the flop?