Sablebrush and SSJones have added important nuances to the OP's question. Estates are terrific for older brands or brands who have experienced former glory years. One of the foci of my collection are Dunhills and Barlings. Dunhills are cheaper AND better to buy from estate than new. (I'm looking at pre-1968s.) And as Sablebrush mentioned, most people's local B&M don't have new 1890 Barlings lying around.
I appreciate why many would be grossed out by an estate pipe, and that's where SS Jones came in well. There are reputable people who restore (and clean) pipes. I grew up in San Francisco and was fortunate enough to work at Sherlock's Haven, proprietor Marty Pulvers. Now retired, he still sells fantastic estates on Pulver Prior Briar. Since I know him, I know I'm getting a sanitized, good pipe. (Check out Marty's website; he's also rather candid about the pipes he's selling, if not too honest, at times.)
I have no worries buying an pipe from Marty (as my pipe racks indicate), nor should you. While I think there are better deals to be had at sites like Marty's and Mike Law Pipes, sp.com and pipes and cigars and others all do the standard sanitizing and restoration. If you're still nervous, do your own research, but estates are the best way to get bang for your buck. Good luck.