The left-wing press will doubtless want to spin this up into a story of chaos and mistrust at the top of government. The BBC’s report, however, is somewhat more balanced and worth reading in full.
https://www.bbc.co.uk/news/uk-politics-49526811
Johnson has the right to refuse to allow the appointment* of any individual to a special adviser role working for any minister. Theresa May did the same to him when he tried to employ one of his former city hall staff.
Whatever they found in her phone logs was obviously serious enough that she needed to have her access and privileges cut immediately. Sajid Javid might be peeved at it apparently going over his head but I doubt this by itself is going to sour his relationship with Boris.
* and therefore also withdraw consent ... i.e. dismiss, sack, fire, etc etc etc