The system itself makes it quite difficult to "Trade" Emperorship as the only way to gain Emperorship is to capture all 6 keeps surrounding Imperial City and the only way to lose it, is to have all 6 of those keeps lost to the enemy. To swap down ownership of the Emperor status in the example noted, you would need a guild willing to participate on an enemy alliance, and also keep the third Alliance from interfering. In our tests internally and in Betas, we've seen once an Alliance gets an Emperor, they really....really don't want to let go of it.
Elder Scrolls can only exist in Cyrodiil "proper" so if you tried to exit the area by going into a Cave or leaving the zone, the scroll would drop. In the pure sense of "sneaking", you can't while carrying a scroll nor mount. Also note that scroll positions are always shown on the Cyrodiil map so as you move carrying the scroll, so does the scroll position on the map.
Some Emperor and Alliance War abilities are useful in standard zones as well as Cyrodiil. Some are very specialized however which prevent Siege damage so obviously, that one isn't useful where Siege isn't being used.
When players first enter Cyrodiil in our Beta's, safety in numbers is the way they go...to start. After a few nights, their tactics evolve and they learn that smaller groups are indeed quite effective in the war not only tactically, but also for fighting other players in the open field. This was mentioned in another question earlier and while small groups can take on larger groups, finding that balance point is something we've been working on for quite some time to give starting players and veteran players they have the option to play how they want to at any given time and have fun. We've seen these smaller groups come out after players get their feet wet and familiar with the game and tactics, and I'm happy to report that I've seen a group of 6-8 players hold off waves of 40 or more at upper levels of Keeps which is exactly what they were designed to do. Eventually they lost, but it proved that small groups can win if coordinated...it just takes a bit of time to develop those tactics.