I've never quite understood why this mission's goal can't be accomplished by using leech weaponry.
Probably because of the way the rules governing leech weaponry were revised between WC3 and WC4. Remember, in WC3, leech guns didn't exist, and leech missiles had a temporary effect. So, no mission objective could really be achieved using leech weapons. I think we can clearly see in WC4 that this basic rule must have governed the mission design for most of the project's duration - that's why time and again you have to kill leeched fighters in order to trigger the next wave of enemies and thus be able to complete the mission.
We may also wonder about when the decision was made to rebalance the game. WC4 is absolutely hardcore in terms of weapons damage - particularly with regards to missiles, it's a far harsher game than any other WC title. This may have been a decision made relatively late in development, in order to set the game more strongly apart from its predecessor (necessary, because the two games used the same engine, and looked very similar). Perhaps until this point, the intention had been for leech weaponry to work on a temporary basis, but with the increased damage from other weapons, leeches needed to be boosted too. So, now the leech missile became a permanent disabler, the guns the same. All of a sudden, it turns out that where the mission originally predicted and provided for one particular way of disabling the Lexington, there was now a second, unexpected way. Not to mention all those other missions where disabling a fighter actually disrupts mission flow. QA would have probably picked up on this, but if it was late in development, I can tell you that the reaction of the programmers and the mission scripters would have been: "we're not changing the scripts, the risk of adding new bugs in the process is too great."
(come to think of it, we do have the WC4 post-mortem document, which includes the list of all the bugs that were not properly resolved - perhaps there is something about leeches in there)
Edit: of course, there is another aspect to it. Disabling a carrier, particularly in this case, should absolutely be harder than simply destroying it. The player should be strongly encouraged to see this as a tough moral choice, where he can either save the Lexington (with great effort and no benefit other than feeling good), or he can take the easy way out and blow it out of the water. But if disabling the Lexington had been simply tantamount to leeching, then it really wouldn't be any harder than sinking the ship, and that effect would have been gone. Now that I think about it, for this particular mission, this is almost certainly a far more important consideration than what I wrote above regarding the changes in leech functionality. In all likelihood, even if it had been planned from the very start that leech weapons will have a permanent effect, we would have seen the other missions fixed (i.e. follow-up waves appearing after leeching of last fighter from previous wave), but the Lexington mission would have stayed the same. The extra complexity of the disabling process is good and useful in this particular context.
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. It certainly showed in UE, but at least Standoff was only as hard as we wanted it to be.