2004 Honda Civic New Noise

Noises problem
2004 Honda Civic 4 cyl Manual 62,353 miles

I bought a this car yesterday. Last time a drove a stick was in the late seventies. Earlier in the day, on the way to my mechanic to check it, I was in 4th gear on the highway and accidentally attempted to shift into reverse because I thought it was 5th! It was just for a few seconds, and there was a brief grinding noise. It didn't go into reverse thankfully, instead it went into neutral. Flustered because I knew the clutch had been fully engaged, I did it a second time the exact same way. Then realized reverse was where I thought 5th was.
My mechanic looked it over & drove it in the parking lot. I told him what I did to it- he said I probably didn't hurt anything because I would know right away if I had. I drove it 30 more miles. Then I noticed what seemed to be a new noise, more noticeable in 1st & 2nd gear- a lower (than the other engine sounds) pitched "rrrr" sound. There is no grinding while switching gears.
Then today I took it to the Honda dealer for an airbag check, and while there, asked him about the noise. He listened to it & said it might be a bearing in the transmission, and mentioned a $1600 cost to replace the bearing.
Now I am concerned I may have damaged the transmission. How likely is that?