It could very well stall the investigation in the FBI, but obstructions have a way of blowing out and DeepThroat 2.0 becomes a result of top level obstruction. We already know DC has been leaking like a sieve since his inauguration. This can very well blow back in Trump's face. Trump has now fired an acting Attorney General and the Director of the FBI (just the second FBI Director ever to be fired). Both were involved with aspects of the Russia connection. And they were fired easier than Flynn, who the Trump team know had "lied" to Pence.
I think it is also important to note that this happened two times in the past. first, Nixon fired FBI director after FBI director during the Watergate investigation... which history shows did not work out so well for him. Then, Clinton fired an FBI director that was brought up on internal justice department charges of stealing money from the government... but Clinton didn't raise the charges, just responded to them.