A few quick relevant items...
Free Action
Free actions consume a very small amount of time and effort. You can perform one or more free actions while taking another action normally. However, there are reasonable limits on what you can really do for free, as decided by the GM.
Attacks of Opportunity
Generally, if you cast a spell, you provoke attacks of opportunity from threatening enemies. If you take damage from an attack of opportunity, you must make a concentration check (DC 10 + points of damage taken + the spell's level) or lose the spell. Spells that require only a free action to cast don't provoke attacks of opportunity.
Free Actions
Free actions don't take any time at all, though there may be limits to the number of free actions you can perform in a turn. Free actions rarely incur attacks of opportunity.
My ruling would be to permit the action, and that getting up from prone does provoke an attack of opportunity. Also, when prone, evasion does not apply.
First off, I appreciate your cite of the rules which lead you to your conclusions. The best rulings, at least in my experience, start with the rules we know, and apply their logic to rule on questions not directly answered. To me, that's the key reason to make a ruling now (in game, to minimize delays), but look it up in detail after the game and adjust as neede for future. In fact, our group has often adopted a policy hat, when working with a new system, you look up the rule even when you think you know it. This helps locate those minor changes between editions (eg. from 3.5 to Pathfinder), even if it means the game runs a bit slower in early play. This also helps those who are, perhaps, less rules-savvy pick up on some of the uncommon (but still frequently encountered) rules.
Prone
The character is lying on the ground. A prone attacker has a –4 penalty on melee attack rolls and cannot use a ranged weapon (except for a crossbow). A prone defender gains a +4 bonus to
Armor Class against ranged attacks, but takes a –4 penalty to
AC against melee attacks.
Standing up is a move-equivalent action that provokes an attack of opportunity.
Helpless
A helpless character is
paralyzed, held, bound, sleeping,
unconscious, or otherwise completely at an opponent's mercy. A helpless target is treated as having a
Dexterity of 0 (–5 modifier). Melee attacks against a
helpless target get a +4 bonus (equivalent to attacking a
prone target). Ranged attacks get no special bonus against
helpless targets. Rogues can sneak attack
helpless targets.
As a
full-round action, an enemy can use a melee weapon to deliver a coup de grace to a helpless foe. An enemy can also use a bow or crossbow, provided he is adjacent to the target. The attacker automatically hits and scores a critical hit. (A
rogue also gets his sneak attack damage bonus against a helpless foe when delivering a coup de grace.) If the defender survives, he must make a
Fortitude save (DC 10 + damage dealt) or die. Delivering a coup de grace provokes attacks of opportunity.
Evasion
A character that has the Evasion ability can avoid even magical and unusual attacks with great agility. If she makes a successful Reflex saving throw against an attack that normally deals half damage on a successful save, she instead takes no damage. Evasion can be used only if the character is wearing light armor or no armor. A helpless character does not gain the benefit of evasion.
Applying the Above
I think it's reasonable to rule that standing up, even as a free action, provokes an attack of opportunity. My own ruling would require reading the ability which provides the rogue the ability to stand as a free action. Looking a little further, I'm thinking this is likely the the rogue talent
Stand Up, which specifically states it still provokes AoO. Given that, and given many rogue talents match or provide feats, I would assume any other feat-equivalent ability to stand as a free action still provokes AoO. Were it not for that rogue talent, I would consider either ruling equally reasonable, but that ability seems to settle the matter from my perspective.
It seems to me a prone rogue does not meet the terms of losing his evasion ability. In fact, it seems qite in keeping with the source material for a prone rogue to roll or tumble out of the way of danger as a use of evasion. While there are drawbacks to being prone, he's still a long way from
helpless.