The presence of an enemy submarine does not make the seazone hostile. So the “Sea units starting in hostile seazones-rules” do not apply.
But from the FAQ we read:
Q. If some of my units begin my turn in a sea zone with enemy submarines and/or transports and I decide to attack them, can I move some or all of my units out of the sea zone in combat movement to avoid having them participate in the combat?
A. Yes. Even though the sea zone is not hostile (it contains no enemy surface warships), you can still move units from the sea zone in combat movement to escape combat if you’re attacking there. However, you must still respect the rules for moving units in the Combat Move phase to escape combat.
This means that in the situation in question, units leaving the sea zone in combat movement to avoid participation in the attack can actually end their movement in friendly zones, so transports that are leaving don’t have to participate in an amphibious assault.
In case you decide to engage the submarine you can do it, but every unit in that seazone that did not perform an alternative combat move will be part of the battle then.
A transport can also load to perform an amphibious assault. It needs an escort in case it unloads in a seazone that contains an enemy submarine.