Julian, as part of a project to ramp up my security, I was about to go with iThemes then decided to try Wordfence first, mainly due to the Wordfence real-time system of blocking attacks based on crowd sourcing, as well as the Falcon cache system. I installed full with Falcon and my site quit working, so I've reinstalled without Falcon and it seems to be going ok. I'll try with Falcon pretty soon, my finger are crossed.
Mark has been helping, but his pace of tech support doesn't mesh with my pace, so things have been going slow in terms of making a decision about keeping Wordfence or ditching it. I did pay for it, so expected it to be perhaps smoother in terms of the install.
There is some overlap in features between iThemes and Wordfence, and quite a few security options can be easily coded without plugin, or done with other plugins. I'm not sure I'd call Wordfence a "replacement," but I'd probably not run both of them.
In terms of disabling iThemes and then running Wordfence, the thing to probably to remember is to fully remove the plugin, not just disable it. As always, do robust backups and disable as many plugins as possible before fooling around with these sorts of plugins that mess with your database. MTN