Heh, no longer sure what the question is. Gonna babble for a bit and hope something makes sense...
Historically, military archers were most definitely warriors, not "rogues" (though in Western Europe at least, professional archers tended to be commoners rather than nobility). Given the amount of training required (crossbows aside), archers were held in some degree of esteem and/or value. How much value varied across cultures, but generally not negative.
The association between archery and stealth comes from hunting, of course - but let's not forget that bow hunting was regularly engaged in by nobility and other upper class folk in various cultures. The hunt was a chance to show one's prowess with the chase and the bow, so again not exactly a dishonorable thing.
The association between archery and thievery always struck me as odd, however - if you're sneaking through windows and other tight spaces, a bow across your back would seem to get in the way... I guess the association was made only because of the stealth connection, or because so many RPGs use Agility or Dexterity to "rule" archery and various thiefly skills.
Skyrim-wise, Archery is considered a http://uesp.net/wiki/Skyrim:Skills skill, but ruled by the http://uesp.net/wiki/Skyrim:The_Guardian_Stones (see notes section). However, the Unofficial Skyrim Patch puts Archery back under the Warrior Stone with the other Combat skills.
If the OP is trying to decide which stone to use, I'd be tempted to decide based on armor, not weapons. Archery can level up pretty quickly on its own - you probably wouldn't really need a boost until you get into the 60s or 70s.
Personally, I tend to choose Guardian Stones for "off" skills - skills that I'll want to level up, but which I won't use often enough to level quickly. For example, I'm running an Illusionist assassin who has the Warrior Stone, strictly for the One-Handed skill. The character uses daggers and occasionally bound swords, but doesn't go toe-to-toe often enough for One-handed to level up decently without help.