Why did Kay leave the children in the unholy and evil environment?

That is a great question, Lana

My two cents worth!

Michael and Kay, sentiments aside....

Michael had already told Kay, very clearly, he won't let her take the children from him that it is an impossibility
Even after that she tells him about the 'abortion' the murder of their unborn child as if

I reckon Kay, a mother, was totally irresponsible to leave the children in the unholy and evil environment, she was escaping from, with the father who is 'blind' to everything other than business

She was unholy and evil too

Kay should have at least taken up the second chance Michael offered and tried to salvage the situation for the sake of their children

[Vito's bonus! an old fashioned traditional wife, Carmela] What a nice pear!
Carmela would never have done, what Kay did to Michael 'abortion' to Vito

Kay became Michael's horror