It's at least arguable that Joel killed the doctor for the same reason he killed Marlene. If the doctor is dead, then there's no one to perform the surgery - or at least one less person willing to perform the surgery. It's one less reason to come after Ellie. I don't know if he did that math or simply thought, "here is someone who was about to kill my girl, and is now stopping me from taking her out of here, he dies".
The notion that he lied to her and therefore must not really love her is completely insane, though.
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"The great promise of the Internet was that more information would automatically yield better decisions. The great disappointment is that more information actually yields more possibilities to confirm what you already believed anyway." - Brian Eno
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