This discussion with you is surely very stimulating, you have found something I hadn't considered, and the prospects are very exciting.
I thought about your counterexample, but I don't think it is a complete system, because the rules given are able to go from (1,1) to (1,2) and (1,1) (as you pointed out), but if you start from (1,2), you can only go to (1,1). This means that there is no rule able to link (1,2) to itself. Adding this rule manually would freeze the system.
Anyway even if this examples may not be perfect, I can finally see your point. The next counterexample you would probably give would be something like the following:
Rules:
{{1, 2}, {3, 2}} -> {{1, 2}, {3, 2}},
{{1, 2}, {3, 2}} -> {{1, 2}, {2, 3}},
{{1, 2}, {2, 3}} -> {{1, 2}, {2, 3}},
{{1, 2}, {2, 3}} -> {{1, 2}, {3, 2}}
Initial Condition: {{{1, 2}, {3, 2}}}
Which should generate a multiway graph like this:

Since there are two ways to apply the rule {{1, 2}, {3, 2}} -> {{1, 2}, {2, 3}} to the state {{1, 2}, {3, 2}}, I have drawn two links.
Now, the issue is subtle, because the two links technically represent the same update event. There are then two possible interpretations:
It may be that the double link is just redundant information. The physics of the system is described by the fact that there is an update event and it doesn't matter how many redundant links represent the event. If this interpretation is correct, the system is frozen, the theorem holds, and I am confident that it holds in every case.
If instead the double link carries a physical meaning (something like doubling the probability of the event), then you are right. Applying every possible rule at the same time does generate a system with an arrow of time, and all the relevant information is encoded in the number of ways a rule can be applied to go from a state to another. (This gives me a nice idea, but it deserves another post)
The only way to decide between these two options is to know how to calculate path weights in the wolfram model in order to reproduce quantum mechanics. I think that Jonathan Gorard has worked on the issue, but honestly I couldn't understand what solution he may have found.
If you can tell me more about it, I would really appreciate it.