Not Sure How To Handle This

Meredith enjoying a warm, clean coop.

Last Friday I moved Meredith's coop to the winter headquarters.  She is snug against the house and protected from the north winter winds.  I installed the heat lamp and reflective shield so she'll stay warm.  I cleaned out the coop really well and put in lots of fresh wood chips so she will be comfortable in there.  The screws to the coop door were coming loose so I replaced them. I filled up her container of food and noticed she has been eating a lot for just a single chicken.  She's been eating as much as two chickens.  Meredith has always been the biggest chick but even accounting for that, too much chicken feed was being consumed.  Later in the day, when I opened the door to take her picture, I found out why the chicken feed has been going so fast.  She wasn't alone in there.  When I opened the door, a chipmunk burst out of the coop and entered the run.  His cheeks were so full that they bulged out on both sides of his face and almost obscured his eyes.  He was trapped in the run.  This explains why I've been seeing this chipmunk around the house so much this fall.  I know how he gets in.  The coop door stays open so Meredith can get fresh air whenever she wants.  The chipmunk is small enough to get under the house and into the run and from there he can go in and out of the coop at will.  I would think, being a small mammal like a chipmunk with thin skin, I would not dare go into a chicken coop for fear the big bird would peck at me.  Meredith has a good 12 inches on him.  She could take him, who ever he is, Chip or Dale or Alvin.  She didn't seem bothered by him.  So is having a chipmunk helping himself to the chicken feed inside the coop a problem?  Could the chipmunk hurt her or give her a disease?  Will he invite his other chipmunk punks over to party?  Will mice or squirrels follow his example?  Or is this not a problem?  Maybe it's a cool story like the lion laying down with the lamb.  Maybe the chipmunk will ease Meredith's loneliness at spending her first winter alone.  Maybe Meredith and the chipmunk are friends like Wilbur the pig and Charlotte the spider.  How am I to interfere with friendship between species?  I am just not sure how to handle this.  Suggestions are welcome.