In those circumstances – when financial institutions that are otherwise perfectly solid are at risk of failure because market infrastructures are disrupted or, more generally, when financial instability originates outside the banking sector – an intervention by the Federal Reserve would certainly be beneficial, and the creation of perverse incentives would probably be limited.
The traditional recommendation for the prevention of financial crises goes back to Thornton (1802) and Bagehot (1873), who argued that, during a panic, the central bank should be a lender of last resort that lends freely at a penalty rate.