This is a perfectly sensible thing to do, and your pages will be indexed just fine.
For pretty much all practical purposes, search engines treat links to a 301-redirected URL just as if the link had pointed directly to the target URL.
Google's PageRank algorithm does shave off a tiny fraction of the rank flowing through redirected links; the amount is apparently comparable to the fraction shaved off on every step in a normal chain of links. In practice, this is not something you should worry about — that time is much better spent making your site's link structure generally easy to navigate, or promoting your site through external links.
Another, more serious, issue is with chains of redirects, where you have page A redirecting to B, B to C, C to D, and so on. Not only does that kind of redirect chaining increase the time it takes for a browser to follow that link, but if the chain is very long, then at some point both search engines and browsers will give up and stop following it. For most browsers, it'll typically takes about a 100 or so hops before they give up, but in this video Matt Cutts seems to be implying that the threshold for Googlebot may be much lower, perhaps as low as five hops.
In any case, 301 redirects are everywhere. Ever visit a directory on your site and have the trailing slash automatically appended to the URL? That's a 301 redirect. Follow a short link to a Stack Exchange question or to a blog post? 301 redirect. URL shorteners? Yeah, they use 301 redirects too. You just don't notice them, because your browser follows them automatically and all but invisibly. If search engines didn't do the same, they wouldn't be very good at crawling the web.