This is in principle a good point to raise, but it is not possible to have migration path (for migration via voting) to a site in beta, and I thus strongly believe it is not possible to have migration path from a site in beta either (also as there is AFAIK no one-wath path). Thus, this is debate while relevant seems premature at the moment (certainly as regards academia.SE as that site is still in beta, too, but I believe altogether).
As said in comments, moderators can still migrate. Thus, the way to proceed for the nearer future presumably should be to flag the question as 'other' and asking for migration. However, I think initially migrations should only be done in extremely clear cases. What is and is not on-topic is not full decided yet and while a closure is easily reversed this is not really the case for a migration. [One could have costum off-topic reasons, too, but I would wait and see how frequent which type of off-topic actually is before introducing them. Meanwhile, costum closure reason or comments could be used.]
Some more technical points related to comments: the migration paths do not count among the costum off-topic reasons, neither by number nor by the way they are create. The number of migration path is at most 4 (excluding meta, I think). Migration path can only by opened by developpers, by contrast off-topic reasons can be created by site's moderators (one proposes another approves, I think). In general, developpers are very careful when opening such paths. We should not expect to get too many.
Abstracly, I agree that the two most natural pathes are academia.SE and math.SE. However, for the reasons mentioned at the start at the moment we cannot get pathes and thus we might delay the debate until we have more data.