That looks like it should work OK. Do the prongs go either side of the pin and fully down to the bottom of the connector?
Sometimes wiggling the cable and/or pushing the wire up with the tool inserted helps.
Sometimes it needs quite a bit of force to pull it out and having the wire perfectly straight.
The worst one I've done is the Seasonic in my main system and that took a hell of a lot of force to get the wires out.
Are you also having problems with the 4 pin molex plug as well bearing in mind that uses a different tool to the ATX pin remover.
Edit: This is how far the prongs on the Molex ATX tool go in:
