I wouldn't do it.
My oldest son has his father's surname, so does my youngest (different dads) so both my sons have different surnames than me. It bugs me, but they are too young to understand/care about it. It seems a bit stupid to give your second baby a different surname just because it flows better with the name. In that case, I would either pick the name even though it might sound bad with the surname, choose a different name, or change the whole family's surname.
I know a couple people who have done various alternate naming schemes. I proposed several to my ex (alternating btwn our names for genders, having an altogether different name, etc), and he wouldn't go along with any of it, so my eldest has his father's last name. The current one being incubated is a solo project, and will have my last name. It bothers me more than it will them.
I think it would be annoying to have to explain why over and over again, e.g., to the people who work at your kids' school. Even if something is none of someone's business, people tend to be curious.
As far as I remember, you've said in previous posts that you want two kids total, right? Not that the number of children makes a huge difference, but I was one of two kids and something like that would have fanned the flames of sibling rivalry for sure. I would have taken it as yet another piece of evidence that my mom loved/identified with my brother more.
Plus, please don't be terribly offended by this but it is just kind of a weird thing to do. One of the biggest reasons I am extremely glad to have had a sibling is that there was a sort of lifelong friendship that came from growing up together, and ultimately (to my surprise) I was proud of the public association with my brother. He was super annoying and evil when we were little; once we reached high school and college I was glad he was my brother and close friend.
This is currently under negotiation with my partner, we're looking to do a gender split, much like the 'son of/daughter of' system they have in Iceland...
I think it took him by surprise at first, but when we discussed it further he understood that it is as much a compromise to me that not all my children take my name as it is will be for him (possibly more, after all their contribution to making and delivering a baby (though necessary) is five minutes of fun, it's the women who suffer).
Kids are smart enough to understand, you just have to explain if they ask. They will know they are siblings. Your family is what you make it, not what you name it.
@rowangreeneyes- What if you use both your surnames? So it would be Rowan blank blank. That is what my older sister wants to do with her future children. If not, I do not think its weird or wrong to use yours. I know some people may frown upon it but if you are not bothered by people maybe assuming your children are not related then I do not see what is wrong. It is your bub so your choice IMO. No one else has the right to judge.
I am glad you found a happy medium! I am not sure what his last name is but I love all the names in your signature for your Rowan's future sibling they are bound to work with his surname.