Divorce means you possibly get murdered, Walter's a psychopathic drug kingpin working with the cartel who, for all she knows, has probably gotten a lot of people killed already.

Divorce is also usually a long and convoluted process in the US, I assume it is in NM too. At the very least it would have put some eyes on them and made other people (including her DEA AGENT BROTHER) confused and possibly looking for answers as to what happened suddenly, especially right after they just had their 2nd kid and are seemingly happy together despite Walt's cancer diagnosis. At that point she didn't want Walt getting arrested (possibly because that would also completely shake up her own life), she was just waiting for him to die of his terminal illness so it'd all be over soon.

It's always crazy to me when someone suggests that a person stuck in a dangerous relationship just breaks up/divorces/leaves. That's not how it works.

Her divorcing Walt would just be completely illogical and serve no purpose other than introducing a whole lot of new worries and complications in her life. As far as she was concerned, Walt would die of cancer in a few months and that'd be that. She didn't want to bring more risk into it than there already was.