Some rec leagues have a running clock that stops on every whistle in the last 2 minutes. Never heard of one that stopped the clock after a made basket.
As for "physical" games: some of these leagues are long on testosterone and short on skills. You can try calling it tighter, but they're often neither smart nor skilled enough to adjust. Then you get a 2 hour game that ends 2-on-2 because everyone has fouled out. No good options.
To the OP: crap like you've been dealing with is the reason why many of us stopped doing wreck ball and never looked back.