A swordsage does have bastard sword proficiency, but not the way you mean
As a swordsage, you are proficient with [...] martial melee weapons
A character can use a bastard sword two-handed as a martial weapon.
In effect, the swordsage has “Martial Weapon Proficiency (bastard sword),” but not “Exotic Weapon Proficiency (bastard sword).” This means that, technically, Weapon Focus’s prerequisite is fulfilled. Even without the discipline focus feature, a swordsage could take Weapon Focus (bastard sword) as a regular feat.
Your character must have the indicated [prerequisites] in order to [...] use that feat.
Technically, the requirement is only “proficiency with selected weapon,” not specifically “proficiency with selected weapon as it is being used,” so RAW you qualify and can use Weapon Focus even when you’re using the weapon in a way that results in a non-proficiency penalty. In that case, you would just take the −4 penalty on attack rolls for non-proficiency, and the +1 bonus for Weapon Focus. A DM may very well block the usage of the feat in this manner, though; I would ask before counting on it.
But a swordsage doesn’t have to worry about that if he’s using discipline focus for this because he gains only the benefit of the Weapon Focus feat, not its requirements. This wording is unusual, and actually quite awkward (does “qualifying for a feat or prestige class that requires Weapon Focus” count as one of the “benefits of” Weapon Focus?), but here at least it clearly means you do not have to worry about requirements for choosing or using the feature.
A swordsage does not have spiked chain proficiency—and this case is more what you meant
If you had asked about a spiked chain, instead of a bastard sword, and had cited Shadow Hand instead of Diamond Mind, then the answer would be a much clearer no.
Bonus feats may be obtained without meeting their requirements. When you do so, however, that just means you get them and can use them despite not meeting their requirements, not that you automatically gain those requirements.
For example, consider a wolf-totem barbarian’s Improved Trip:
A 2nd-level wolf-totem barbarian gains Improved Trip as a bonus feat, even if he doesn't meet the normal prerequisites.
Improved Trip [General]
Prerequisites Int 13, Combat Expertise.
The wolf totem feature that grants Improved Trip allows you the following benefits:
You do not provoke an attack of opportunity when you attempt to trip an opponent while you are unarmed. You also gain a +4 bonus on your Strength check to trip your opponent.
If you trip an opponent in melee combat, you immediately get a melee attack against that opponent as if you hadn’t used your attack for the trip attempt.
I.e. the benefits of Improved Trip. It does not suddenly give the barbarian 13 Intelligence, or the Combat Expertise feat.
In exactly the same way, a swordsage who chooses Shadow Hand gains the benefit of Weapon Focus (spiked chain), but this has nothing to do with the feat’s requirements: he doesn’t have to, nor does he automatically, meet its requirements. Which makes sense, since the feat not only requires proficiency in the spiked chain—which the swordsage hasn’t got—but also BAB +1, which a 1st-level swordsage would not have regardless of weapons chosen unless multiclassed.
The swordsage would be able to use the benefit of Weapon Focus (spiked chain) with Shadow Hand discipline focus even with a spiked chain he is non-proficient in, of course: −4 for non-proficiency, +1 for Weapon Focus.