I'm currently rewatching this, and just started season 6. Knowing how it all ends helps to see the nuance in the characters I didn't catch when it aired. Megan is not bothering me as much because I can now see how badly Don treats her from the jump. Don makes the same mistakes with Megan as he did with Betty, and it is interesting to see how she reacts differently. Because Don never really confronted why his marriage to Betty fell apart. It was easier for him to think Betty left him over the whole Dick Whitman thing and not his controlling behavior or his affairs. Even then Betty was willing to overlook the affairs as long as they happened in Manhattan (or on a business trip) and did not interfere with their life.
I see why Don wanted to marry Megan and thought himself in love with her. Don is a shit dad and needed a partner to take care of his kids when he had them. Dude couldn't even handle every other weekend. Then Don heard Megan wanted to try being a copywriter, and he envisioned a future where his work-wife was actually his wife. They get married and he just dumps Megan into Peggy's lap to deal with. Of course, Megan worked only when Don wanted her to work. I get why Megan wanted an out from that work environment. I do think the groundwork was laid in seasons 4 and 5 that Megan was not completely honest with what she wanted. A running theme of this show is that what you think you want is not really what you want. Megan put aside her childish dreams of being an actress, but she still wants it. She was lying to herself and Don in Tomorrowland when she said she had given up on that dream. I do think, though, that a better actress would have been able to portray this clearer.
Unpopular opinion here, I think Megan is just as childish and immature if not more as Betty. I know Don needs to be called out for his controlling behavior, but her hissy fit in the Howard Johnsons was not the way to do it.