It will still have backpressure... just may not be the right amount.
They can run without a pipe, but not very well and hot due to a lot of the fuel going right out the exhaust because the pipe isn't there to push it back in. It's a timed pressure thing (tuned).
The resonator I bought off ebay (stock jato 3.3) is an open single chamber pipe. Basically a hollow tube inside. But usually, pipes built with a baffle in them are built to keep it, but I'd run it and see how it does anyway.
How did you get it out without ruining the pipe?