I think it would be a HUGE mistake to let "LORE" get in the way of making a good game/mod
From my understanding the FS Team are fully aware of this and will use "LORE" first and foremost - but if this gets in the way of making the game playable, balanced, and FUN then I believe exceptions will be made
As a massively sweeping statement and generalisation **puts on flame retardent suit**
LORE would lean towards having the EMPIRE with larger numbers, "better" vehicles and technology, and some highly skilled and trained parts of the army
The REBELS would be far fewer in number, have inferior weapons, vehicles - however they would have a small group of 6 "heroes" and "the FORCE" on their side
This is very difficult to effectively program into the game as you could not unbalance the numbers in the game, give the team with better numbers all of the best ships - I think I would be able to predict which side would keep winning in the games!
It would be difficult to ensure that the best players get on the smaller team to counter-act all of this - e.g. do you program "the FORCE" to allow REBELS to get lots of "lucky shots" 
I know that the 6 heroes play no part in FS but I think that the wider audience needs to be considered to ensure that FS is successful on as big a scale as possible
I would say the vast majority of this "wider audience" have just seen the films and are not "lore" experts
Therefore I think that "LORE" should definitely be used as the guiding principles BUT not to the exclusion of good gameplay IMHO