As most of us would know, you SHOULD only be able to hit those [Freaky] eyeballs inside of her when she drops down. Namely, only when she uses her web to attach herself to the ceiling. So after she finally falls down, you then would normally use the vine brush technique to attach the blossom vines to her... But I've found a quicker alternative.
Instead of doing the above mentioned, just use the vine brush power right away.
To do so, first press square directed either to the left or right to obviously start dashing. It doesn't honestly matter which way you go or take, but as I'm right-handed, I found it easier to start dashing left. You can either just leave it at that, or dash until Amaterasu gets even faster, at speed level two. It is needed, but it'll be simpler if you're fast enough to evade the queen's attacks. One of which being where she'd rush over to you and use this web shot, or where she'd run over and start smashing into the rock floor. Either way, you're running so she shouldn't be able to even touch you, so once you're at the side of her, facing her sideways, immediately use vine on her hooks. Don't go to far behind her though, she'll just automatically turn around and you won't be able to trap her. After getting one vine on her already, repeat it twice more, like the usual method to get her abdomen to release. But be careful and mind the falling rocks she causes to drop from the ceiling; they obstruct your brush in order to paint. Don't take too long either, she'll break free from the vine(s). You've now discovered a faster way to kill her.