You can't use a melee weapon as part of a ranged attack, it's impossible.
You can't use the javelin as a melee weapon.
However, the precedent DracoSuave pointed out is the Wizard of the Spiral Tower ruling in the FAQ.
The question is to the effect of "When a WotST uses a longsword as an implement, can he apply his Weapon Focus feat to the damage of the attack?", and the answer is "Yes".
The WotST is not using the longsword as a weapon; he is using it as an implement. However, the longsword is a weapon. Therefore, the feat, which adds to damage rolls with his chosen weapon group, applies, even though he is not using the longsword as a weapon.
The javelin is a melee weapon; while it is being thrown, it may not be used as a melee weapon. Intelligent Blademaster doesn't care if you are using it as a melee weapon, just as Weapon Focus doesn't care if the WotST is using the longsword as a weapon; Intelligent Blademaster only cares if it
is a melee weapon.
While being thrown, the javelin is a melee weapon that may not be used as a melee weapon, and it is also (effectively) a ranged weapon.
In the absence of this FAQ ruling - for example, if the FAQ changes to say that Weapon Focus only applies to damage rolls when you are using your weapon as a weapon, or if you hold the FAQ ruling to be incorrect - I think the weight of support is in favour of Intelligent Blademaster being inapplicable to a thrown javelin. But if one accepts the FAQ ruling as valid, then it follows that Intelligent Blademaster applies.
-Hyp.