That was my point.
Before my K1, I had a valid ESTA and used it to visit my now-husband. Once my 129F had been filed, approved and sent to NVC, it was all in the system and it was a risk (albeit low, for me) to travel at that stage as CBP could see my immigrant intent. However, I went to the POE fully loaded with evidence that I would return (employment, property lease, etc). The application in itself does not affect things, she will not face denial purely because she applied for/gained a tourist visa. It is all about how it is perceived.
If your MIL is ever asked at B1-B2 stage if she plans to immigrate to the US, she must be honest.