Honestly, I do not know
It is very hard to say - the layout may work just fine (depends how it looks). Normally, I would try to avoid to go into this kind of situation from beginning, now it may be hard to try to improve it.
As you correctly noted, what the tracks on L1 will be doing, you do not know. I am not sure how the L2 looks (how good reference plane it is), but layout on L1 in this case may influence EMC/EMI results.
What to do? Depends how much time you have. If you are in hurry, you may try to build your board as it is. In the worse case, you may slow down the memory (?) but your software guys may still be able to use the board for software development. And later, if you also make improved version of your board, it could be interesting to compare EMC/EMI tests between them.
If you feel bad and you are not sure, then re-do the layout.