All you ever have is a probability. Sometimes, the probability is so large that we pretend it is absolute, but it never is. Philosophical point aside, the issue is not whether there is direct or indirect evidence, it is what the evidence suggests happened. I believe the relevant standard is more likely than not. If you look at all the data and it suggests that they were more likely than not deflating the balls, then it doesn't matter if the evidence is direct or indirect.
The science doesn't prove tampering, but it doesn't rule it out either.
Let's look at a few other indirect things.
McNally's official job responsibilities did not include preparing, inflating or deflating footballs. It was that of another guy. McNally took the balls without permission of the referees, which allowed him to have access without an official nearby. What was he doing? He should not have had the balls at all.
McNally lied about going to the bathroom when questioned.
McNally/Jastremski exchanged text messages about Brady being unhappy about the PSI in the game balls.
McNally/Jastremski exchanged text messages about providing a "needle" and about how there better be "cash" or he would overinflate.
McNally/Jastremski exchanged text messages about how Brady felt McNally "must have a lot of stress trying to get them done."
McNally/Jastremski exchanged text messages about how the refs "fucked us" by inflating them.
McNally/Jastremski exchanged text messages about "not going to ESPN, yet"
The Wells report simulated the conditions and could not repeat the pressure difference.