I send transactional emails from my application on my customers behalf. I\'d like for the receiver to be able to click reply and have the reply go directly to my customer, witho
Provided your sender address is properly set and matches your DKIM/SPF DNS records, you're correct that a reply-to should not negatively effect your sender reputation.
But ultimately it's a provider level decision, so YMMV across different inbox providers.
I was able to find the answer at another location http://www.quora.com/Does-sending-emails-with-a-From-address-with-a-different-domain-from-the-Reply-To-address-hurt-ones-deliverability
Apparently the reply-to header can be set to another domain without any threat to the deliverability of the email. On some of the smaller mail admins this may cause a problem, but technically speaking its perfectly legitimate.