We accept checks online. The way that we have it setup, they simply run the check through and then we automatically take the amount via a draft each month. It works well for us, especially for local clients, but we've got a few outside our area that work just as well.
If you don't trust your processor, then you should definitely find another one. Having another company processing your payments is built on that basic foundation of trust. If there isn't complete confidence in them, then basically you're just waiting for the day where they justify why they aren't to be trusted.