The basic problem is that the two sides are never going to agree on the object of knowledge or standards of evidence. Science, whether conducted by Christians, Hindus or atheists, seeks to find and quantify the regularities of nature, the aspects that are uniform over time. Religion looks for unique events that signify the hand of God. Science, by its nature, dismisses miracles, even when it can't explain a phenomenon. This is simply the way it works -- always assume that events are the result of uniform laws. The assumptions and thought processes of scientists are automatic in this regard.there really isn't ever going to be a science that seeks to prove miracles. The scientific mind is always going to assume that unexplainable phenomena are simply not yet understood.
Returning to the topic of the proposed agreement: We can tone down the rhetoric and remove name-calling from the threads, but we are not going to eliminate the friction caused by questioning each others sources and witnesses.
We already know lots of euphemisms for much of that list, but the Internet Flame-Troll is a fairly new concept. We'd have to invent some new term like "Master at Baiting People."