My instinct would be the same as yours, for 'plant-fungus,' purely on linguistic grounds, because you don't have a familiar adjective form for 'plant' available. A more balanced pair might be something like, er, 'vegeto-fungal,' both equally latinate and inflected. But 'vegetable' is highly ambiguous (broccoli, spinach), I don't think there's any such prefix as 'planto-' or whatever, and I'm not aware of any other Greek or Latin root or prefix with quite that meaning.
So 'plant-fungus,' with two nouns used as adjectives, is at least understandable at a glance, and sounds a lot better than an unparallel construction. If you need formal support for your decision, the English style rule is that similar concepts should be expressed in parallel form.
Of course, if you were writing for a general audience rather than scientists only, 'interactions between plants and fungi/funguses' would be better still. (-: