I've been at this for about 20 years and I have to agree with your Realtor. Will you recover your expenditure? I think the more accurate way to phrase it is, how much will the buyer want to discount for the mismatched floor? Even if they don't mind it that much they will probably want to use it as a bargaining point. As for a flooring allowance, I don't recommend it. I had a listing with very dated carpet and the seller wanted to give an allowance. I got a bid to replace the carpet and put it in with my brochures advertising an allowance. Showings but no offers. Finally the seller just replaced the carpet with a neutral color throughout and the house was under contract within two weeks. Most buyers don't want to move in and do work. Those who do want to be substantially rewarded for their efforts. Hope that helps.
If in your judgement, this will increase the sale ability of the home or increase the amount it sells for it may be worthwhile, otherwise list it w/o changing it.
Your agent's recommendation should be considered.