DO NOT DO A FACTORY RESET WITH A CUSTOM RECOVERY OR ROM!!!
::deep breath::
Using Titanium Backup is probably the easiest way, but you don't need it for this.
You can delete any keyboards you want. What you need to be sure of is:
1. You have a properly working and configured replacement to use as you keyboard input method. In other words, install your keyboard of choice and be sure it works before deleting anything.
2. When removing system apps, you back them up properly, just in case.
If you have your preferred keyboard installed and selected, you should be able to uninstall others using Menu >> Applications >> Manage Applications >> All tab, selecting it and clicking uninstall. If it is subdued then you will have to do the following:
1. Use your favorite root explorer enabled file manager and mount /system/app as read-writeable.
2. Find the keyboard apk(s) that you wish to remove. Copy it/them to your SD card; a separate folder is helpful.
3. Delete the Swype (or other) apk from your system/app directory.
4. Reboot.