As far as I know you can.
You can use Advance Config (use search function on XDA or Google to find it) to disable Threaded SMS. As TouchFlo has it's own settings (even with font etc), it should not affect the way TouchFlo shows your messages.
Just give it a try. Be aware that you have to install .NET (Compact) Framework 3.5 to get Advance Config (3.3 is the latest) working.