Are you stating that your wife's employer has not decided whether it will respond to the RFE or simply fire your spouse?
Your wife is not accruing unlawful presence while her extension is pending, but if her employer decides to cancel the extension and terminate her employment that can change very quickly. The difficulty here is that you have told us that her I-94 expired on March 12, so if the employer abandons the effort to get the extension she won't be able to change her status due to her expired I-94 - once her I-94 expires she can only utilize COS if the extension is approved.

