There will -always- be flaws. However, part of a company selling security is how they respond to issues, and here, BlackPhone has performed quite well. There was a problem, they fixed it, and that is what matters.
I agree that how a company handles incident response is important and the BlackPhone guys have apparently handled this well.
However, there are several things that are troubling about this story which lead me to not trust BlackPhone and question the security experience of the people designing it.
The first thing we notice about this exploit is that the library in question appears to be written in C, even though it's newly written code that is parsing complex data structures straight off the wire from people who might be attackers. What is this, 1976? These guys aren't programming smartcard chips without an OS, they're writing a text messaging app that runs on phones in which the OS is written in Java. Why the hell is the core of their secure messaging protocol written in C?
The second thing we notice is that the bug occurs due to a type confusion attack whilst parsing JSON. JSON?! Yup, SCIMP messages apparently contain binary signatures which are base 64 encoded, wrapped in JSON, and then base64 encoded again. A more bizarre or error-prone format is difficult to imagine. They manage to combine the efficiency of double-base64 encoding binary data with the tightness and simplicity of a text based format inspired by a scripting language which has, for example, only one kind of number (floating point). They get the joy of handling many different kinds of whitespace, escaping bugs, etc. And to repeat, they are parsing this mess of unneeded complexity .... in C.
Compare this to TextSecure, an app that does the same thing as the BlackPhone SMS app. TextSecure is written by Moxie Marlinspike, a man who Knows What He Is Doing(tm). TextSecure uses protocol buffers, a very simple and efficient binary format with a schema language and compiler. There is minimal scope for type confusion. Moreover, the entire app is written in Java, so there is no possibility of memory management errors whilst trying to read messages crafted by an attacker. By doing things this way they eliminate entire categories of bugs in one fell swoop.
So yes, whilst the BlackPhone team should be commended for getting a patch out to their users, this whole incident just raises deep questions about their design decisions and development processes. The fact that such a bug could occur should have been mind-blowingly obvious from the moment they wrote their first line of code.