First off, the Equinox EMH did retain his loyalty, so it would have stood to reason that our EMH (from now which I will refer to as 'Our Doctor') would do the same. However he didn't seem to try to help his crew at all; he was about to kill Seven, who was his friend. Even for selfish reasons, a rational mind unbounded by ethics would choose Seven over the crew. Even if it was simply, in his own words, because he would have to find another singing partner otherwise.

This never made much sense to me.

So I have come up with a little theory. The doctor had no intention of harming Seven and was just playing an act, biding is time for rescue. The removal of his ethical subroutines did not make him willing to kill his friend, but just made him more willing to cause her distress for his own selfish reasons. From 'I cannot cause any harm to Seven' to 'I can cause some harm to her now to save her in the end'.

My evidence is as follows:

• He did not cause any major harm to Seven, despite having more than enough time to.

• He was under close watch by the Equinox crew, unlike the Equinox EMH who was thought to be our Doctor and had free reign.

• Our Doctor was in love with Seven, morals or no he would not have killed her due to that reason and that reason alone.

• As soon as he was transported to voyager/was in friendly territory again, he disregarded all the loyalty and orders he had previously been given, made a short speech about the room being his sickbay, and deleted the Equinox EMH. The fact that our Doctor deleted the Equinox EMH instead of deactivating him is proof that his ethical subroutines had not been restored.

His comment about being Mr. Hyde could have been more about his willing to hurt Seven at all, than being instantly loyal to the Equinox and willing to kill her.

All in all: Our doctor was biding for time, with his new sense of (or lack of) morals, he made the rational decision to harm her now to bide for time and save her later. He may have also came to the conclusion that if he hadn't pretended to go along with the orders, he would be deactivated (which of course he would not want) and the crew themselves may have attempted to harm her (which, in a twisted sense, he may have felt that only he should be allowed to harm her at all). I don't believe he had any intention of killing her. He also remained loyal to his crew; he just had his hands tied. As soon as he had the opportunity he again showed loyalty to his own crew over the Equinox.