Has there ever been any evidence that this was once a binary system?
None. The Sun matches the behaviour of similarly massed stars very closely. While about half of all stars are in multiples (and so about 1/3 of star systems are multiple), no evidence of the Sun having a companion star has been reported.
If a putative companion were comparable in size to the Sun, than we'd see it by night. In fact, we'd not really have a night. (ACC played with that in one of the Space Odyssey sequels, IIRC)
If th putative companion were smaller than the Sun, it'd have to be considerably smaller to not be obvious. Smaller stars develop more slowly and last for longer, so it would still be visible. That relation lasts all the way down to the bottom end of "stars" at around 80 Jupiter-masses, when we get into the brown dwarfs. And even for them, we can model the evolution of temperature (from heat released on formation from infalling material) against time, and say "there isn't anything bright enough out there". (We do have adequate whole-sky IR surveys.)
Get down to Jupiter-mass and smaller (Brown-Batygin propose a Planet 9 of around 10 Earth masses/ 1 Neptune mass/ 0.03 Jupiter mass) and the temperatures and luminosities continue to decrease, but remain potentially observable (Brown has recently been complaining about the weather on Hawaii, blinding his telescope time looking for exactly this). Unfortunately, there are other similar-looking sources on the sky, at greater distances than the putative Planet 9, which is going to complicate interpretation of the data.
Astronomers do not reject the idea of "the Sun's companion", "Niburu", or whatever you want to call it out of caprice, malice to SF authors, or because their Mufti tells them to. The hypothesis has been rejected because observational evidence that should be visible if the hypothesis were correct has been looked for and is not there.