One good way to do an incomplete-but-pretty-good sterilization is to start the plant growing in the way it was in the natural environment e.g. submerged or emerged, and then slowly add/remove water. If the plant tolerates it, cycle this a few times from no standing water to covered in standing water. This should activate many parasites' responses to water stress - encysting / hibernation - and then deactivate. Many parasites can only survive one or two cycles.
Or try growing in chlorinated tap water, changing water every day to freshen the chlorine. A super dilute bleach solution may provide similar cleaning action.
If a floating/rootless plant, just switching the water often will probably go a long way.
Of course all of the above will stress most plants, but doing it slowly so as to allow for plant growth at the same time should allow collection of many wild species.