The plan as of right now is that the WWE will indeed go ahead with the first ever women’s Money in the Bank Ladder Match at the Smackdown Live Brand Exclusive PPV.
Unless there will be any changes, as of the moment there will be two women’s matches on the card: a championship match with Naomi facing the winner of next week’s five way match and then the aforementioned Money in a Bank Ladder Match which would consist of all the other remaining women in the roster.
A women’s Money in the Bank Ladder Match was very close to happening in last year’s show as it was discussed for last year’s PPV, but ultimately it was nixed.

WWE’s initial format sheet for the Women’s Match on the Money in the Bank PPV in June simply indicates “Women’s match #2”. This would imply that while the match is definitely planned, it is by no means confirmed.
Source: Wrestling Observer Newsletter