A&A Sea Zone Attack Rule Clarification
The guidance from the updated 2005 Europe rules almost assuredly applies. You MAY take losses on allied units even when on the attack, and furthermore, MUST take them if there are not enough attacking units to take all the losses. Allied subs may NOT submerge as they never rolled dice. Quote below:


  When German subs are attacked in a zone that contains Allied naval units of more than one nationality, Allied losses can be taken from any of those Allied vessels. If the defending German subs score more hits than the attacking player has ships, must the excess hits be taken from the Allied ships that are standing by? For example, a sea zone is occupied by three German subs and two British transports. The US player brings in two destroyers and attacks the subs. The German player rolls his defensive dice and scores three hits! Must the Allies lose three ships, even though the Americans attacked with only two?
  A guiding principle throughout the rules is that if there is a way to apportion hits so they result in losses, the losses must be taken. In this case, the Allies must lose three ships; whether those are two destroyers and a transport or two transports and a destroyer is up to the Allied players.
  
  In the previous example, what if the British transports had been subs instead? Could they submerge to avoid becoming casualties?
  The only time subs can submerge is immediately before rolling dice, whether attacking or defending. In this example, the British subs can't submerge because they don't get to roll dice (they're not defenders -- Germany is defending, the US is attacking, and the British are just innocent bystanders caught in the crossfire).