Joel was always a bad guy, just depends on your personal perspective.
He lied to protect her but i think she knew.
Absolutely, Marlene would have healed up and came after them.
Killing Ellie in that procedure was a long way off being a guaranteed cure/vaccine. Ellie should have been given the choice to die for that chance or chose to live, they kept her sedated and were going to kill her without having discussed it with her so they all deserved to die in my opinion.