Presumably the government can advise the Queen to withhold consent. And unlike withholding Assent, there's much more recent precedent for it (again from Wikipedia).
In 1999, Queen Elizabeth II, acting on the advice of her British Cabinet, refused to signify her consent to the Parliament of the United Kingdom debating the Military Action Against Iraq (Parliamentary Approval) Bill, which sought to transfer from the sovereign to parliament the power to authorize military strikes against Iraq. This prevented the bill from being debated. In 1988, the Palace of Westminster (Removal of Crown Immunity) Bill could not be debated in the British parliament because Queen's Consent was withheld, as with the Reform of the House of Lords Bill in 1990.
Also note (same source):
If consent is required but not signified, a bill may make no further progress through parliament. If a bill is mistakenly allowed to progress even though the required consent was not signified and the error is discovered before Royal Assent has been given, the proceedings may later be declared void.
But again, the news is that opposition is refusing to grant the PM the general election he desires until the Benn bill has received Assent (not merely consent); and after the latter is granted consent can no longer be withheld.
The gaining of Royal Assent for the bill was a requirement that Labour leader Jeremy Corbyn said his party would need before it considered backing Mr Johnson's call for a general election.
And more particularly, Bercrow (the Speaker of the House) has ruled out that consent was needed for this bill.
Sir Bill Cash, the Tory Brexiter, asked if the bill required Queen’s consent. Cash said he was inspired to ask the question partly by this blog by Robert Craig, a public law lecturer, who suggested Queen’s consent would be required. He argued that this would be a problem.
But Bercow told Cash he had considered this matter and decided Queen’s consent was not required.
I'm not sure of the exact route how this ruling could be appealed, but presumably the Queen can overrule him at Assent time, if Bercrow was somehow in error on this.