De Gaulle was always much more in favour of an intergovernmental organisation than supranational one when it came to running the EEC and even if the Conservatives were to sign the Treaty of Rome I'd see them being natural allies on this point, which being two of the three heavy hitters would carry a lot of weight. If what became the European Parliament stayed indirectly elected and the European bureaucracy much less powerful I think you'd see a much slower push towards federalisation.
Speaking of De Gaulle he apparently threatened to withdraw France from the EEC in 1963 during disagreements with Germany over the newly proposed Common Agricultural Policy. Now it wasn't a genuine threat as shown by the fact that when the Germans called his bluff he didn't follow through, but what if he had? He withdrew France from NATO's unified command only two or three years later. If he did withdraw France then due to a combination of stubbornness and French parliamentary and regional elections coming up so not wanting to be seen as u-turning it would probably be a couple of years before they rejoined. The CAP is likely still introduced but in a more limited fashion, perhaps with say a limit on its cost as a percentage of the EEC's budget and having to be renewed in ten years time or lapse. With no French participation it would shift the organisation in a more free-trade minded direction, ideally laying the groundwork so that when France rejoins they simply have to accept it. Periodic renewals of the CAP, and increasing its budgetary limit, could be bartered for expansions of free trade between member states.
Where would De Gaulle's temporary replacement Gaston Monnerville (in a De Gaulle assassination scenario) or any potential successors (in a scenario where De Gaulle is not killed off) likely stand on the EEC? Did any potential candidates share similar views to De Gaulle with regards to the EEC in preventing anything resembling the EU from forming except keeping the EEC strictly economic / free trade / no tariffs / etc or even any anti-EEC candidates besides De Gaulle's threats to leave?