My wife was out on maternity leave from Nov. to Jan. for the Birth of our son. During this time the company gave all employees the standard (for the company) holiday bonus. My wife was told that she would not receive a bonus because she was on leave at Christmas (Only after she asked). In the past they have pro-rated bonus' for employees who did not work the whole year but were there at holiday time. (IE when my wife started in March, she received a bonus the following Dec for 10 months). It seems to me that had she been on leave from Sept-Nov that she would have gotten a bonus.They clearly stated that it was because she was on maternity leave at Christmas.

It is a small family run company, about 25 employees, and we have had other small problems with them related to the pregnancy and employee rules differing for family.

My question is---
Is not giving her a holiday bonus a legal issue or just immoral?

Let's forget about past years for the moment.

THIS YEAR, did employees on non-FMLA leaves receive the bonus, or a pro-rated portion, or none at all?

She was the only one out on leave.

In that case, previous years would come into play and I would think it worth her while to discuss it with the EEOC and/or the state human rights commission.

Just a thought, but given the size of the company she was not "entitiled" to maternity leave through FMLA therefore this leave was given at " the pleasure of the Company" per se.

Given that, would there still be an expectation of no negative actions because of it?

I can't say for sure that there will or will not. But at 25 employees they are subject to the ADA and pregnancy is a covered characteristic, so it will be on the employer to show that this was due to a change in policy and not due to her pregnancy.

Makes sense to me, OP let us know how this works out if you choose to persue it.