Though in a subservient position, the Gibeonites could still influence God's people, and their gods eventually ensnared the Israelites. Through deception, Joshua's exception to God's command to drive out the Canaanites set a precedent that allowed other pagan peoples to co-exist within Israel, ultimately leading to her downfall.
In all these events, a tension exists between God's sovereignty and man's choice, between God's will and "free will." Within the Christian zeitgeist floats an idea that because God is sovereign, everything that takes place must be His will—that if He wanted something different, He would have caused that other course instead.
Indeed, God is sovereign over all, and He does guide events according to His purpose. However, not everything happens because God has willed it, especially where sin is involved. We must differentiate between what God allows—a great deal!—and what He truly intends, desires, and enjoys. He has allowed countless sins that He could have prevented, yet Scripture rarely shows Him preventing someone from sinning or acting foolishly. He clearly does not intend or take pleasure in sin, but He allows it. He says to choose life—that is His will—but allows us to choose death (Deuteronomy 30:15-20).
The events relating to the Gibeonites show that God allows matters that do not please Him to play out. Though they are not what He intends, He will still bring about His purpose despite them. We must be careful about ascribing human behavior—especially human sin—to God, concluding that it must be God's will, or it would be different.
As we know, the ends do not justify the means. When it comes to doing God's will, how we do things can be just as important as what we accomplish. Cain concluded that one offering was as good as another, but God rejected it. Nadab and Abihu thought any fire would work for God's altar, and they died instantly and shockingly. How we do things determines whether God accepts the result—whether it is truly what He desires and pleases Him or whether He forebears as He does with countless other acts. How we act affects what we produce.