You can manually disable lens flares separate from the other graphical settings by editing GraphicsConfig.xml in the elite-dangerous-64 directory (or by pasting the relevant section into GraphicsConfigOverride in the game directory in your user profile).
This is what the segment looks like:
Code:
<LensFlares>
<Off>
<LocalisationName>$QUALITY_OFF;</LocalisationName>
<Enabled>false</Enabled>
<QualityIndex>0</QualityIndex>
<ImportanceThreshold>2</ImportanceThreshold>
</Off>
<Low>
<LocalisationName>$QUALITY_LOW;</LocalisationName>
<Enabled>true</Enabled>
<QualityIndex>0</QualityIndex>
<ImportanceThreshold>2</ImportanceThreshold>
</Low>
<Medium>
<LocalisationName>$QUALITY_MEDIUM;</LocalisationName>
<Enabled>true</Enabled>
<QualityIndex>1</QualityIndex>
<ImportanceThreshold>1</ImportanceThreshold>
</Medium>
<High>
<LocalisationName>$QUALITY_HIGH;</LocalisationName>
<Enabled>true</Enabled>
<QualityIndex>2</QualityIndex>
<ImportanceThreshold>0</ImportanceThreshold>
</High>
</LensFlares>
You can just set all the "Enabled" segments to "false" so no matter what quality setting you use, lensflares are off.
I would also recommend turning down the "GlareWeight" values in the Bloom segment. Half of the defaults keeps some bloom but looks much more natural.