You are not considering the implications of congress interfering in a relatively minor state matter when it refuses to legislate on more pressing state/federal issues (gay marriage, legalising cannabis, etc).
[1] http://en.wikipedia.org/wiki/Commerce_Clause
Be careful with the word 'always'. If a federal law were unconstitutional, and an equivalent state law were not, then clearly it would not trump the state law.
Similarly, despite the modern interpretations of the Commerce Clause, there are Constitutionally imposed limits on federal authority, and they're prescribed a very narrow set of privileges by the Constitution. Depending on the law and its execution, we could very well see a state exercising its rights trump the Commerce Clause. Gary Marbut has fairly carefully crafted such a challenge with his "Montana Buckeroo" rifle which is expressly designed, built and sold only within the confines of Montana, specifically to challenge the Commerce Clause's authority of its manufacture.
That said, he's got some 80-odd years of precedent to overcome, but there may be a quorum that much of that precedent is bad precedent, though it's still a gamble as to whether or not that matters.
While I personally agree with Mr. Marbut's interpretation of the commerce clause's limited scope, I think that the deck is stacked squarely against him, especially since Raich.[1]
I'm not sure if you're being serious or just completely ignorant about how bills are passed into law. Clearly, a Republican controlled House will not vote in favor of gay marriage or legalizing cannabis. Heck, almost every Democratic state hasn't even legalized cannabis and there are still a good number of Democratic states that haven't recognized gay marriage. Those won't pass the federal level any time soon.
"Minor" issues, by the way, are passed into law all the time because both houses can agree on the bill. Take the JOBS Act or the Pay Our Military Act for instance.