Yes, evil eye stacks with the pinned condition. The penalties are untyped and come from different sources, so they stack.
All told, you should be looking at −2 penalty from evil eye, a −4 penalty from the pinned condition, and it is denied its Dexterity bonus to AC by the pinned condition as well, potentially reducing the AC yet more.
The rules for tying someone up only specify that it makes someone easier to pin, but the helpless condition specifies that a helpless creature is one that is “bound” (or several other things), so in answer to the title question, yes, the creature should literally have had the helpless condition, even though the rules for tying up themselves neglect to mention it. For the purposes of the rest of this answer, however, I will presume that the helpless condition was not applied for whatever reason, since if it is all of this becomes moot—against a helpless creature, you can coup de grace, which doesn’t even use an attack roll, automatically crits, and has a chance to flat-out kill the target even if the crit damage wouldn’t already have been enough to do that.
As for more you could have done, an easy one is knocking the target prone, if it wasn’t already; that gives melee attackers a +4 bonus on their attack rolls. Another easy thing is flanking, since the target is pinned anyway; even if the second flanker didn’t even try to attack, he could have given the samurai another +2 bonus from the flanking. Finally, the last easy, everyone can do it thing I can think of is the aid another action, which everyone (aside from the samurai himself) could have been doing to give the samurai a +2 bonus each. With three such helpers, plus the flanking and prone bonuses, the samurai would have gotten an extra +12 on his attacks.
There is undoubtedly more you could have done, or at least someone could have done if they had the right tools, feats, or class features, but it doesn’t really matter. If you cannot hit a target with −6 or more penalty to AC while you have a +12 or more extra attack bonus, you shouldn’t be attacking, you should be running. Even if for some bizarre reason this thing was unable to escape that situation (which nothing that powerful should be without some kind of escape button, but whatever) and you actually managed to kill it, something that powerful is likely to have powerful allies, which may well mean someone will resurrect it and now it’s pissed at you personally.