The short answer is that dictionaries are both descriptive and prescriptive, always with an uneasy balance between the two. You can argue that the word “marriage” *should* not be used to describe same-sex unions, but you cannot argue that it *is* not being so used.
I learned while working on my Master's degree in English that dictionary creators have always looked to examples in print to determine definitions. If you start with the OED, which used to contain a written example from each decade the word has been used, lexicographers look to how the word is being used. Thus, dictionaries often reflect their time.
My lexicography professor, incidentally, earned his Ph.D. in divinity from Harvard in the 1930s, was an ordained Episcopal minister, and was one of the hundreds of editors of Webster's Third International Dictionary. He would have agreed with the definition, despite his personal preferences and background. If you look at the literature of the past decade, the concept of same-sex marriage has been so prevalent in the media and literature of the time, is it any wonder that this particular definition appeared.
The problem is not the dictionary; it is the importance we are placing on the dictionary.