Cryptographically speaking MD5's pre-image resistance is already broken, see this paper from Eurocrypt 2009. In this formal context "broken" means faster than brute force attacks, i.e. attacks having a complexity of less than (2^128)/2 on average. Sasaki and Aoki presented an attack with a complexity of 2^123.4 which is by far only theoretical, but every practical attack is build on less potent theoretical attack, so even a theoretical break casts serious doubts on its medium-term security. What is also interesting is that they reuse a lot of research that has gone into collision attacks on MD5. That nicely illustrates Accipitridae's point that MD5's safety margin on pre-image resistance is gone with the collision attacks.
Another reason why the use of MD5 in 2009 has been and now the use of SHA1 is strongly discouraged for any application is that most people do not understand which exact property the security of their use case relies on. You unfortunately proved my point in your question stating that the 2008 CA attack did not rely on a failure of collision resistance, as caf has pointed out.
To elaborate a bit, every time a (trusted) CA signs a certificate it also signs possibly malicious data that is coming from a customer in form of a certificate signing request (CSR). Now in most cases all the data that is going to be signed can be pre-calculated out of the CSR and some external conditions. This has the fatal side effect that the state the hash function will be in, when it is going to hash the untrusted data coming out of the CSR is completely known to the attacker, which facilitates a collision attack. Thus an attacker can precompute a CSR that will force the CA to hash and sign data that has a collision with a shadow certificate only known to the attacker. The CA cannot check the preconditions of the shadow certificate that it would usually check before signing it (for example that the new certificate does not claim to be a root certificate), as it only has access to legitimate CSR the attackers provided. Generally speaking, once you have collision attacks and part of your data is controlled by an attacker then you no longer know what else you might be signing beside the data you see.