I don't think changing the points from 40 to 30 or 25 would makes a difference with the problem you're showing, Komo. Let's take the example you show here

Lose 141, win 5 is the case right now.
If we change it from 40 to 25, that's 37.5% less. (or 62.5% of the original; 40*0.625 = 25)
If we apply the same change, you'd win 0.625*5 = 3.125 points
You'd lost 141*0.625 = 88.125 points.
Overall, that's a loss of 85 points.
Yup, that's less points

Still a large amount. But the problem lies somewhere else.
Let's look at the score you put up: CF has 6712, cFc has 6508
Now, the starting point is 1000. This means CF is 5712 points above it. Now these points also are different

5712*0.625 = 3570, so CF's new rating becomes 4570.
cFc's new rating becomes 1000 + (5508*0.625) = 4442.5
At first sight, the difference between the two clans looks smaller.
But let's see how big a chance it really is

Say you need 10 wins to bridge the gap. 204/10 = 20.4 points per win (current situation)
Now, we go to the new situation: the difference is now 127.5
The amount of points per win is 20.4 * 0.625 = 12.75
So even though the difference is smaller, you'll still need 10 wins.
As for the win percentage, franz pretty much sums it up in his last line

win percentage only tells you something if you know who they played against in those very games. Scoring 50% against Random is a far better result than scoring 50% against me

So it's fair for there to be a better reward for scoring 50% against Random than for scoring 50% against me.
As for having more points by having played more games: I'm afraid that if we want to solve that (not sure whether it's a real problem or just cFc playing more difficult opponents here), a simple shifting of numbers isn't going to do the trick (for the reason I explained above), we'd need a new overhaul of the rating system entirely.