The Doctor wouldn’t. He’d find another way.
right, instead he’d just GENOCIDE THE DALEKS INSTEAD.
because that’s FITTING
Because the 7th Doctor totally didn’t attempt to wipe out the Cybermen, in their entirety in Silver Nemesis.
Nor did he talk what seemed to be the last, or one of the last, Daleks to death in Remembrance of the Daleks.
And his third incarnation didn’t slaughter an entire army of Daleks via ice volcano in Planet of the Daleks.
And the 6th totally didn’t wipe out the vervoids.
And the Doctor wasn’t totally convinced he’d wiped out TWO species, including his own, prior to the 50th anniversary. The Davies era Doctor wiped out both the Daleks and the Time Lords, along with whatever other legions of combatants were involved in the Time War.
Sure, the Doctor will give a warning, an option to go otherwise from time to time, but if a species is nothing but murder, he will try to put a stop to it, or at the very least not interfere in its destruction. The 9th didn’t see the alternate universe Cybermen as a new species that needed protecting or guiding. He wiped them out (well, he tried). The Racnoss? Wiped out. Last of the Great Vampires? Finished off via starship impalement. The Krotons? Acid into the vats, dead to the last drop.
The 10th Doctor’s plan in Journey’s End was to use the reality bomb to kill the Daleks instead of everything else. It may have been his clone that executed said plan, but it was the plan from the start.
That doesn’t even touch upon the unique creatures that he killed, attempted to kill or, in some cases, worse-than killed. Axos and the Family of Blood didn’t come away easy.
Even if you go back to the 4th Doctor being given the opportunity to wipe out the Dalek race before they arose (considered by the show runners to be the unintended opening salvo of the time war), it was not out of concern for the Daleks that he didn’t do so. It was because he was afraid of what the change to the timeline would do to innocent races and empires.
Past the initial couple of clashes, the Doctor takes every opportunity to wipe out the Daleks when he encounters them, failing to do so only when he is unable to or when doing so would cause harm to other beings. This applies to the cybermen as well, and anything else irredeemably parasitic, predatory or murderous. Especially if they threaten his pet species, humanity.
If anything, having the Doctor space-fold a planet out of the way of a massive Dalek assault, causing the Daleks’ weapons to blow themselves up, is relatively chill for the Doctor.