I don't have enough experience with Omaha, but let me ask this: If either blind didn't have enough to cover, or if a limp caller didn't have enough to call, how do you calculate a pot sized raise?
Whatever rule you apply there should also be applied to the small blind that is less (all the way less) than what it should be.
Frankly, I think it should be the full 700.
To use Hold 'Em as an example, when a big blind is all in for less than the BB, it's still a full BB amount to limp call.
Therefore, in the original question, I think the full amounts should be used to calculate the pot sized raise.
On a somewhat related note, I played in a $1/$2 PLO game at Aria a few years back. It had an interesting twist: The amount to call was $5, any raises had to be in $5 increments, and the $3 total blinds were rounded to $5. That meant if the first player wanted to raise pot, it was $15 rather than $7. Not only did it help raise to a more meaningful amount, but it made the math easier once the pot grew.
For the record, I'm not sure if the blinds continued to be rounded up or were rounded down if one blind folded.