One of Stephen King's better known pieces of advice is to murder your darlings. You know, those beautiful passages that you absolutely love. The pieces of your heart and soul put into words. Moments of brilliance that are beyond the scope of mortal man and therefore must be divinely inspired.
The ones that make betas roll their eyes and give you weird looks... and when someone gives you a weird look by email without so much as showing their face, you should probably take heed.
As with any murder, this is a wrenching and messy ordeal full of agonizing internal conflict while your better self tries to stay your hand. But you know that you must overcome that impulse for mercy... the darlings must die. Sacrifice the one for the many and make your writing stronger for it.
The potential victim doesn't want to be done in. It will try and plead its case and make you feel as bad as possible for this heinous act you're contemplating. It will beg and plead (not exactly sure how those are different, but usually when one is begging, they're also pleading, so I'll go with it). The more shrewd darlings who have the "fight" as well as "flight" responses may even threaten you with the destruction of your precious vision should you excise them. But there's a distinct power balance involved here and you have to remember who's in charge - you or your words?
For those of you with mouthy darlings who refuse to go quietly, shut them down with one of those "sayings" that angry parents like to threaten with, but never follow through on:
"I brought you into this world. I can take you out."
After the deed has been done, you have to remember to clean up the scene. Police your rounds and leave no evidence of the deceased behind to make future readers wonder. Darlings are tricky things, and all it takes is one allusion later in the MS for its ghost to shriek to life reminding the world of what you've done in the name of your craft.
If done properly, you are the only one who will have to shoulder the burden of your act. Your beta is merely an accomplice, the look out, if you will. You're the axe man and this isn't something you can put off on someone else. Their darlings won't be yours and you might end up with the wrong victim on your hands and hard drive. Mistakes like that lead to the plot police and open graves called plot holes... bad stuff to get caught with. A job done well is the kind no one ever notices.
Now get out there and get that manuscript under control.
Knock 'em dead.