The 12th Amendment was written in response to a major problem encountered in the 1800 election. The Constitution (Article II, Section 1) originally stipulated that each of the electors would vote for two people for President, and the VP would be the recipient of the second-highest amount of electoral votes for President. In 1800 there was a tie, and it took 36 votes to finally elect Jefferson as President.
With the 12th, Electors are directed to vote for a President and for a Vice President rather than for two choices for President.
As two separate offices, the disqualification of either the President or Vice President doesn't affect the other.
So, no, the "entire ticket" is not disqualified.
Are you saying that an Obama disqualification would result in McCain as Pres. and Biden as the VP?