I've been using the PHB II Affiliations rules in my campaigns for years, and we've always enjoyed them. I recommend involving the executive powers in play as soon as possible. Perhaps the guild boss could consult with the PC before using such a power, perhaps an Affiliation score of 15 puts the PC on a council that votes on whether or not the guild boss can use these powers, or perhaps the PCs are simply victims or beneficiaries of executive powers. The point is to make executive powers appear in the campaign sooner rather than later. For one thing, they're fun, but also, they will appear unnatural and out of place if a previously sleepy world suddenly sees an outbreak of plagues, shadow wars, and crusades simply because a PC reached a 30 affiliation score.
As the rules in the chapter say, creating an affiliation is more of an art than a science. The guidelines and samples presented in the chapter are exactly that: guidelines. As Col Pladoh says, "It is the spirit of the game, not the letter of the rules, which is important."
About the "free benefits," while it is certainly possible to write down an affiliation that gives benefits for free, I wouldn't advise it. Instead, I think that the benefits an affiliation grants should be balanced by duties, obligations, and violent threats: mandatory tithing, assassination attempts as you rise within the guild, enemies made because of you joining the guild, study (place a number of ranks in an otherwise "useless" skill), and so on.