I probably shouldn't answer this until I am in front of the computer and can look at the files LOL, but the quick and dirty answer is - Eagles are a pain in the ass.
So that file and block is the correct area to get rid of eagles. The ONLY sure fire method is to completely remove the lines in there. Bontainer's example is actually one where I was trying to fiddle with the results to reduce eagle's but unfortunately none of those experiments worked.
If you remove these two lines:
There will be very few (almost none) eagle attacks on players (or even NPCs). You will still encounter an eagle at one or two points of interest and you will still occasionally encounter eagles swooping down and carrying off prey (monkeys, pigs, goats, etc.) as those prefabs are different.
Every encounter in Far Cry is a "prefab" made up off distinct pieces. So for example you always get 2 guards escorting 2 prisoners down a path. The game spawns two guards and two prisoners and randomizes their appearance using "kits" to define how the various characters and creatures can look.
The prefab however handles all the necessary characters, vehicles and other items (for example bombs in the bomb disposal karma encounters) and defines where to place them - how far apart, what angles, what alert status, etc.
Vinh and I tried to modify the pagans wrath prefab which always spawns 3 trucks and 6 guards (3 drivers + 3 gunners), but it never changed in game so either the files are ignored or like many things in far cry there are other files which also have to be adjusted to get it all working. I forget at the moment which file names the game uses for handling the prefabs, but I remember there is at least 3:
1) The file listed above which is a master spawn list basically.
2) The file which lists all of the prefabs and everything contained in them.
and
3) The individual encounter archetype files which presumably also contain the necessary info to spawn the opponents and objects. These unlike most archetype files cannot be decoded using the normal gibbed tools. I was never able to adjust these. They CAN however be renamed resulting in swapping one kind of thing for another - a trick I used in Far Cry 3 to make cargo trucks and dune buggies spawn where cars normally would and vice verse.
At the moment the EASIEST and most consistent way to mess with spawns is to use the file bontainer listed above. There are entries for almost everything that spawns randomly in game. Unfortunately you cannot adjust some things - for example the buzzers that spawn outside the first outpost or the Ghale family homestead.
Regarding the weight values - I have had a lot of trouble with these. They don't seem to work as I would expect (at least not consistently). Normally in most games that use a weighting system the weight of an item is compared to the others. So say one creature - lets say an eagle has a weight of "1" and the other perhaps a crow has a weight of "3" then the game SHOULD be three times more likely to spawn crows than eagles. In Far Cry however no amount of adjusting weights would alleviate Eagle attacks to any great degree. Much more testing needs to be done here to figure out how the game actually uses weights with regards to spawning. My gut instinct and limited testing has me thinking that Far Cry will ALWAYS spawn everything in the list entry at least once no matter what the weights. Maybe that is to keep variety going and keep the random number gods from having you run into the same two honey badgers over and over again. Again I'm just not sure, but it needs to be tested.
Like everything else we have limited control over this aspect of Far Cry. Do not be afraid to experiment however and report your findings