Whether or not this deal goes through remains to be seen, but I wouldn't take Jose's comments as the gospel truth. How many times over the years did we hear Sir Alex state, very clearly, that we wouldn't be doing any business, only for a transfer to be announced a short time later? Jose could well be speaking truthfully, but it's just as likely that his comments were calculated.
Personally, I don't think the past several weeks will have significantly changed Jose's opinion as to what our defensive needs are. If he believes that Lindelof is that big a talent, and an upgrade on Smalling, Jones and/or Rojo, then he'll want to bring him in while he can. I have a feeling that Jones has really found favour with Jose, as he spoke publicly about Jones' bravery in declaring himself fit to play after being out for so long (not to mention his quality performances), but I'm not so sure he fancies Smalling and Rojo long term. Smalling, in particular, just seems to lack the steel that Jose loves in his central defenders.