One of our "herds" is pretty much the exact same as this- two horses, pastured together for about a year, then a pony added a few months ago. From my own experience, and from what I was told even before I brought the pony home, no, it's not likely they will ever be best buds.
For the first while, the "middle mare" would attack the pony whenever it got within 40 feet of her, and after she ended up hurting herself while trying to hurt the pony, I put a stop to it. After I punished her for going at the pony, all the severe aggression has cleared up.
By now the formerly aggressive mare and the pony will eat at the same round bale and graze together etc, but it's still fairly obvious that the two horses have a little friendship together and they tend to "exclude" the pony-like a bunch of little girls on the playground
Basically, long story short, horses will be horses in the pasture. I personally don't want mine pinning ears at each other or fooling around when I'm within 20 or 30 feet, but some people do. If the horse doing the chasing is well trained, I wouldn't worry too much about it-she may not display any aggression when she's on a halter/lead or saddled. If she does start being aggressive when you have her out of the paddock, be sure to punish her.