As far as Flynn goes, possibly. But if it can be proven that Trump knew members of his cabinet were compromised but didn't do anything about it - it could absolutely be used against him in the courts (if/when it ever comes to that), since it would be disgustingly negligent of him as President.
Does that mean Trump was unwitting?
But even then, if it comes out that a number of his closest confidants were colluding with Russia and he had absolutely no idea it was happening, it makes him look like the biggest idiot on the planet. Neither scenario paints him in a good light. Especially since he often brags about how smart he is.