The problem is you have a non-synchronized transmission; it has nothing to do with whether or not you have live PTO. (You don't.) As long as the transmission input shaft is spinning, the gears will clash when you try to engage them. Even if you disconnect the PTO, there's enough friction in the clutch to keep the input shaft spinning.
With that in mind, it should be fairly obvious what to do: Before engaging the PTO, first put the transmission into the desired gear. If you need to shift gears while mowing, always come to a full stop before shifting; that will stop the input shaft and PTO from spinning.
There are tricks you can use to shift a non-synchro transmission on the fly; you can double-clutch or shift without using the clutch at all. These techniques allow you to control the transmission input shaft speed using the engine. It's simpler on your tractor just to come to a complete stop, as you really need a third arm to double-clutch anything with a hand throttle.