That was my interpretation as well... that Jacob saved Sayid's life but couldn't save them both (for some reason?)
I don't think Jacob wanted
to save them both. Jacob clearly had designs on Sayid. Just like he had designs on everyone. Jacob, above all else, wants to serve the island. So if Nadia has to die, who gives a fuck?
By the same token, Kate's airplane toting buddy Tom needs to die too because he needs to meet a tragic end to get Kate where she's going.
I think it's inaccurate to assign benevolence or malevolence to Jacob because he's probably just a force of nature.