I went and read the FS1 cutscenes in the wiki and realized that the quote from Alpha 1 is a little more complex than just stating that the Shivans are THE Great Destroyers. Rather, he actually states:
Long had we been the destroyer.
Which implies that there can be more than one destroyer, or that there can only be one destroyer, but who it is can vary. I think an abject analogy would be the cleaning guy who scrubs disinfectant on everything. He kills all the bacteria, but he also preserves the sterility of the environment, so new bacteria have an easier time evolving and adapting to their environment without mass competition. Those bacteria would also serve to sterilize the environment if they faced any (weaker) competition.
So yeah, in this case the Shivans were the great Destroyers and the Vishnan the preservers, but it may be that either can serve the other's purpose at any time, they just have a tendency to appear to do one thing to the races they encounter because they are so powerful. For all we know the Vishnan may be on the verge of annihilating another species that the Shivans protect, who know the Vishnan as the Great Destroyers.
It's not exactly implied by the Shivans getting kicked off the Grand Council for going too far, but for all we know it could be one big political snafu over conflicting ideologies between the Shivans and the Grand Council. Maybe the Shivans are the Great Nonconformists.
Also interesting is his statement:
I'm told we can expect them again, but not in my lifetime.
Bumbumbum...BP tie in? After all, who would be telling Alpha 1 that he can expect the Shivans or not that he would trust?