We recently had a situation that we can not seem to get a
cut and dry answer to.

A's ball 2nd and 5 from their 20 yard line, A passes over the middle to the 27 yard line where B36 interferes with A88. B48 then intercepts the pass and then an inadvertent whistle is sounded.

Ruling, since B had the ball, they have the choice of taking the play to that point, they are then penelized 15 yards from previous spot, 1st and 10 for A at the 35. Or they choose to replay the down. NF 4-2-3c

Or Ruling that A gets the choice of replaying down or accepting PI then 1st and 10 for A at the 35. Case book 4.2.3 Situation B(a)

What would you rule and why?

First you deal with the penalty. If it is accepted, you are done. If it is declined you deal with the inadvertent whistle. The option belongs to the team in possession at the time of the whistle. They can accept the result of the play or replay the down. In your case, A would most likely accept the penalty for PI.

The best thing that can happen when there's an IW is to have a penalty.