In a local league game because of windy conditions bails weren't used at either ends. The bowler disturbed the wickets with his legs before collecting the ball and running out the non striker when the second run was being taken. No stumps were removed from the ground on both occasions. Was the batsman out? This video here is exactly how it happened except the player involved was the bowler and not the wicketkeeper.
Yes, this is a valid dismissal once the decision was made to play without bails. Law 29.4 makes this very clear:
After a decision to play without bails, the wicket has been put down if the umpire concerned is satisfied that the wicket has been struck by the ball [...] or by a fielder in the manner described in 126.96.36.199.
(where 188.8.131.52 is "by a hand holding the ball").