Yeah, that bugged me too. You easily could've cut the scene down, or removed it entirely, without impacting the plot at all. "OH THIS CHARACTER IS A KID DIDDLER, HATE HIM" he's already a cunt, we get it.
It's also really hard to care about the Winterfell plot, not only because both Stannis and the Boltons are irredeemable at this point, but because it honestly doesn't matter anymore. Whoever wins, they're going to be assaulted by Littlefinger and the forces under the royal banner. It's not even the fact they killed Shireen that bothers me- it's the fact they killed her in a manner that completely undid character development.
I could believe it if it was Selyse and Melisandre, since they've been at best antagonistic and cold to the kid, but Stannis? C'mon, you've literally spent the last two years building up Stannis' awkward, but affectionate, relationship with his daughter. It makes no sense.
Doesn't help that the circumstances leading up to it- Ramsay somehow managing to destroy basically all of the weapons and reserves without being noticed and riding out without being noticed- is shitty writing.