They have cast companions who have appeared on the show in the past, so I don't see much of an issue.
Companions that have been on the show before don't bother me as I can easily dismiss it as two distantly related people in two separate time periods. It's not implausible that distant relations will have similar facial features. It's a lot harder to get into that thought when it comes to the Doctor himself for obvious reason.
Moreover, Torchwood became increasingly separate from Doctor Who with the last two series, so it's not a big issue for me.
Capaldi being great as he is, I'm sure he will play the role in a unique way different from those roles.
Torchwood still exist in Doctor Who universe. The Torchwood cast has appeared in actual Who episodes, so it's not that easy for me to just dismiss characters in that series.
Hey, I agree that Capaldi will be good in the role. I just wish he hadn't already played characters in Doctor Who and Torchwood.