Warp drive? More like WMD
Looks to me like we will have a nice little weapons platform to use on them littel grey guys from Zeta Reticuli.
No but seriously this doesn't seem like an insurmountable problem perhaps some sort of reversal of the warp field before you enter into a solar system to jettison the built up particles out into empty space.
Going over the math it appears all you really would have to do is slow your acceleration as you get close. As in start using a smaller and smaller warp field. It seems to me your planet destroy is going to happen if you just shut the field off.