I dont think this is a patch issue...itsa diplomacy issue. The reality is (just like in real politics) you'll get in massive trouble if you try to be friends with everyone. Just doesn't work. You need to be selective with who you sign pacts with. As an example, I was playing a game as Portugal....I was friends with Indo, Poland, and Poly. I was at frequent war with Rome and Babylon, and sometimes Japan. Egypt was playing it smart refraining from battle, simply building wonders. anyway, they were the first to adopt an idealogy - Order. Jap, Bab, and Rome all followed suit. Indo and Poland adopted Auto. After this, Poly and I established a Def Pact, which actually helped against my war with Babylon more than once (and yes Poly was actively helping). After Poly adopted Freedom, I decided to go Auto, but I did not make any pacts with Indo and Pol. Long story short, I ended up winning a Diplo victory, but was very selective with choosing Friends and making pacts.
The issue with Defensive Pacts backfiring on you if you sign to many actually reminds me of another great game - Knights of Honor, by Black Sea Studios. A very underated game, it pits you as a medieval power in Europe/Mid East/Africa, where alliances and trades were contantly shifting. My first game I tried to be friends with everyone, but in the end I ended up alone with no friends and all enemies. It just cant be done; you have to be selective and strategic with your diplomatic choices.