My gut feeling is that the MVC model, or, for that matter, any cleanly defined model, tends to decrease security risks. Although things are not that clear.
From a very general point of view, security issues are a special kind of bug, on the implementation or on the structure (possibly the specification). Knowledge dilution is a huge risk factor: bugs happen more often when there are more people involved in the project. To keep the whole thing secure, there must be someone, at some point, with a transverse view of the project, who can think architecturally and grasp the interactions between all the modules; this becomes harder when the project size grows. To say things in plain words, for a secure Linux kernel, you need a Linus Torvalds: one head who receives all the information.
Any clean model which defines the roles and tasks of sub-modules in a clear way, such as the MVC architecture, will help that one-thinking-head a lot. It makes it possible to maintain the necessary project-wide security thinking framework, when the project becomes huge. On the other hand, the MVC model encourages throwing more developers at a project, which mechanically increases security risks, so MVC is a mixed blessing.
As a basic rule, the smaller the project, the more secure it can get. The Lone Wolf Developer model will get you more secure applications, and probably will deliver them faster, but with less features.