In the 2004 Revised Edition rules, there is no specification that if you unload one unit from a transport as part of an amphibious assault, that you must unload both units. (if the transport happens to be carrying two.) There is in fact a clarification in the game's FAQ on the Wizards Of The Coast websote:
From the Wizards/Avalon Hill Axis & Allies Revised FAQ:
Must I offload all the units from a transport?
No. Units may stay on board when other units offload. For example, one unit may offload during an amphibious assault, while another may offload into the same territory during the noncombat move.
However, the Larry Harris Tournament rules state that if a transport is unloading units into the land portion of an amphibious assault, all units onboard that loaded as part of this Combat Move must unload and participate in the combat. Any units that were onboard the transport prior to the Combat Move phase (from a previous turn, in other words) may be selected to remain onboard the transport.
From LHTR v1.3
Amphibious Assaults: A transport may begin or
take part in an amphibious assault by
offloading at least one of its cargo units
into a hostile territory during the combat
move phase. If it does so, it must offload all
units that have been loaded during this combat
move phase, and it may offload any number of
units owned by the transport's power that
already were on board at turn start. If enemy
sea units are present in the sea zone in which
the transport is to offload, a sea combat must
be fought first. If the transport survives
that combat, then after all defending sea
units are destroyed (or submerged), it may
offload into the hostile territory.
It's an interesting question... I think that the LHTR version is best, because any unit that moves during the Combat Move must do so with the intention of being involved in a Combat. In this case, it is the unit being loaded onto the Transport that is the initiation of its Combat Move. It has committed to combat. Loading onto a Transport during the Combat Move phase seems to count as only half of the unit's Combat Move, and the second half must be carried out as planned, ie the "assault" part of the Amphibious Assault. Any unit already onboard the transport has technically not moved in the Combat Move phase, even if the Transport does .
You do seem to be a bit confused about the Infantry's ability to load/unload though. Infantry (ditto Armor and Artillery) IS allowed to load, travel on a transport, and unload into an Amphibious Assault Combat on the same turn.