Or maybe your intention was to enable/disable the filtering on demand?
While off, there will be some reverse bias B-E voltage sometimes but not enough to damage the transistor.
With the transistor on, C-E will be low resistance in both directions like an analog switch.
I suppose it may work.
But there is a problem with off: while the collector may go positive with no issues, if it tries to go negative it will forward bias the BC junction and pull the base below the emitter.
As said above, the BE junction won't break down with merely -3V, but the base drive circuit will source current into the base and then the collector.
To make it really off, the base drive circuit needs to have high impedanece even when taken below ground. For example, a common emitter PNP.
An N-ch MOSFET would clamp drain voltage to -0.7V due to its body diode.
CMOS switches probably have some diodes too and likely wouldn't stay open circuit below ground, unless supplied by a -3.3V rail.