lens flare to my knowledge is for lens flare. The color comes from the surroundings and an expected whitish flare.
You might instead be interested in using lighting effects.
Or better yet, try this out.
Create two layers.
color one red using the paint bucket.
Now on the second layer, it should be above the first in the layer order, use any other color. Green works well. use the paint bucket to color this layer green too.
Good, you should now have one red and one green layer. Use the lens flare on the green layer. good.
Now comes what may interest you.
You see how for each layer you can adjust the layer mode, in the top left of the layer window you'll see a drop down list. By default it uses NORMAL.
Instead of NORMAL, choose VIVID LIGHT, or LINEAR BURN.
See if that helps.