.....since "real" ecommerce sites don't run ads as well?

Sure they do.  Haven't you seen ads on amazon.com?  They are called "product ads from external websites" (look low on the page on right side).   Ebay has lots of ads.  Hayneedle stores have ads (look at bottom of page).

I run ads on my ecommerce sites and block ads from direct competitors.  I vary their position depending upon how much I want to throttle my sales.

....I have a site now on precious metals which is high-content, low amount of adsense...

Adsense does better for me with precious metals content than affiliate links.  But, then it will depend upon the type of content that you have.  Some topics inspire shopping more than others.  Of, course the PM sites will gladly buy links from you.... but I am not a seller.

I was thinking I might choose one metals broker affiliate link (like a Goldbank or someone) and place it in the sidebar. Would that small change screw up my rankings?

Probably not... if you nofollow the link.

And, "a site with a shopping cart operated by the affiliate program" I'm not clear on this. Why is that?

It makes you look like a retailer instead of an affiliate.

Affiliate sites get hit mainly because they are usually just signposts for someone else.

If you want to survive as an affiliate build a content site with a store, a content site with affiliate links instead of ads, or a site with a shopping cart operated by the affiliate program.

"Your site wont get any penalties as long as your site was indexed first."

Who is indexed first  does not matter.  What matters is who has authority.  Authority often wins even if last published.

Lots of affiliates are really really smart people.  If you require them to use rel=canonical they will know what you are doing and what the result will be.  So, if you have great affiliates don't do this to them unless you want to risk losing them.

I am an affiliate and if the program manager told me to rel=canonical my pages to his I would reply.... "you point your pages to MY site or I am leaving".

I would not be linking to them either because their product might go through a shopping cart on my domain.

If I ran an affiliate program and had very valuable and smart affiliates I would produce new content for my own site that takes me out of competition with the affiliates and let them know that they are free to use the data feed or create their own unique descriptions.  But that descriptions on my site are off limits.

You don't want your superaffiliates jumping to the competition or becoming your competition.  They are not married to you and even if they are they will file for divorce.

Subdomains are often viewed by google as different domains.  That means, links that hit one of them benefit that subdomain but transfer fractional benefit to other subdomains and to the root.

If this was my project I would use folders instead of subdomains.  Your designer can make them look unique if that is needed, however, with them all being in the root directory all of the incoming links will benefit the entire site.

In early 2011 I redirected two subdomains of a busy site (one more powerful than the root domain) into folders and the results have been kickass.  Kickass.