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A fleeing non-SM unit rallies/'regroups', within embarking distance of a friendly transport.

Now, can that unit then embark?

Relevant pages:
page 46 "Regrouping"
page 66 "Embarking"

As long as their 3 inch move brings all of them within 2" of the access point on the transport they can embark.

Regrouping does not disallow them the ability to embark.

They can move up to 3 inches after they regroup, after that they can not move further but they act normally.

I can't see anything that would stop you from doing this outside the normal embarkation rules.

as death said as long as every member of the group is within 2 inches of an access point sure thing.