Washington State Attorney General Bob Ferguson released a formal Attorney General's Opinion (pdf) stating that Initiative 502 does not preempt local governments from regulating or banning marijuana businesses within their jurisdiction:
Under Washington law, there is a strong presumption against finding that state law preempts local ordinances. Although Initiative 502 establishes a licensing and regulatory system for marijuana producers, processors, and retailers in Washington State, it includes no clear indication that it was intended to preempt local authority to regulate such businesses. We therefore conclude that I-502 left in place the normal powers of local governments to regulate within their jurisdictions.
The opinion concludes that I-502's drafters could have structured the initiative to explicitly require local governments allow marijuana businesses, but did not, and that the state legislature is free add this requirement to state law if it chooses. In fact, a bill has already been filed in the state House to this effect. HB 2322 would prohibit local governments from "preventing or impeding the creation or operation of commercial marijuana businesses licensed by the liquor control board."
Formal AG opinions are issued at the request of lawmakers and public agencies, and while they generally guide the interpretation of law, they are not legally binding. That said, a cursory reading of this opinion suggests that it is fairly well reasoned.
UPDATE: The Washington State Liquor Control Board, tasked with implementing I-502, responds to Ferguson's opinion:
The legal opinion will be a disappointment to the majority of Washington’s voters who approved Initiative 502. We’re not yet sure how this opinion will change the implementation of the initiative. If some local governments impose bans it will impact public safety by allowing the current illicit market to continue. It will also reduce the state’s expectations for revenue generated from the legal system we are putting in place.