If it really bothers you, you could always make a sleeve for it out of cloth or leather, and cinch that under the saddle bag. Something that long might look odd there, though. I'm not sure it would be an improvement over just fitting the pump in the frame.

I use Zefal Hpx pumps for the most part. They don't look vintage either, but that's a small price to pay for a pump that functions well. I prefer a pump over CO2 but that's kind of an obvious alternative that is easily hidden.