Exploits fall into roughly two distinct categories: those which break the semantic rules of the implementation language (buffer overflows, use-after-free, uncontrolled type casts...) and those which play "by the rules". Since the new PDF reader is written in Javascript, exploits from the first category ought to be extremely rare, because of the intrinsic protection which is built-in in the language (checked array accesses, garbage collection, strong typing...). To obtain an arbitrary code execution exploit out of Javascript software, you have to find a hole in the Javascript engine itself; holes in the software written in Javascript will lead "only" to an exception, i.e. software crash, which is inconvenient but not as much as seeing your machine hijacked.
Presumably, the Javascript engine in Firefox is thoroughly tested, since it is so much used.
Exploits which play "by the rules" include all the workarounds around the Same Origin Policy and abuse of gateways to local resources. These are not made intrinsically harder or easier by virtue of the PDF reader being implemented in Javascript. However, doing such things right is similar to rendering Web content securely, something which has been a main goal of Firefox for years. We may hope that by implementing PDF rendering in the browser, they will be able to piggyback on all the hard work already done to keep your browser safe from hostile Web pages. At least, when it comes to containing PDF scripts into an appropriate sandbox, I would trust people who've done that for years (the Firefox developers) more than people for whom this is only a secondary work item, distinct from their core craft (the Adobe Reader developers).
So, for security, this new reader actually looks quite promising. Things become better, not worse.