ColdZer0 said
The guy had a low c-bet percentage so I decide to lead on the flop with top pair to avoid a king or an ace hitting on the turn.

When he calls I feel like check-calling is better on the turn instead of betting as my kicker isn’t the best and he could easily have KJ or AJ. He does bet one third of the pot with 1.2k and I call. 

I only have a 4k stack behind now and when I check to him again on the river he bets half pot (3k), I’m not really sure what to do at this point..

This is a good illustration of why betting purely for protection isn’t often a good idea. Sure, you avoid some low-EV spots when the turn card is an A or K (which will happen 16% of the time, less if your opponent has one in his hand) but you create new low-EV spots like this one for yourself. A donk bet is an aggressive pot building technique. If you don’t have a hand that wants to play a really big pot (which might be either a monster hand or a bluff, but not a marginal hand), then you shouldn’t start building one. 

The best way to handle an A or K on the turn is to accept that it’s bad for some parts of your range, like this one, but good for other parts, such as when it pairs you, or when you checked a monster on the flop.