But if it starts to rain, the difference in performance between inters and slicks will also decrease, even if the track isn't fully wet. And if it rains in Malaysia it mostly isn't a drizzle, so it will get wet fast. The performance of the slicks will decrease fast (not to mention the risk of going off), and the performance of inters will improve (relatively). And there will also be a difference in performance between worn inters and new inters.
Let's say it did start to rain on Lap 41 whilst McLaren kept Hamilton out. Alonso was 8 seconds behind Hamilton after pitting at the end of the previous lap. Alonso would gain 5 seconds on Hamilton due to slicks, bringing him 3 seconds behind Hamilton. Hamilton would have the choice to pit for new inters that lap or stay out.
Scenario 1, Hamilton pits for new inters: The track won't be immediately wet so Alonso would have the chance in free air to continue making up time. Up until a point the slicks would continue to be faster than inters, so judging by the previous pace of the slicks it is highly probable that within 2 laps as the track got wetter Alonso could at least make up the 3 seconds he was behind Hamilton when Hamilton pitted. So if the rain did intensify enough for inters, and Alonso pitted he would at least be right with Hamilton when he came out, more likely in front.
Scenario 2, Hamilton stays out: Slicks are still faster than inters for a time so once again Alonso will be right with Hamilton if not in front whenever they both decide to pit for new inters.
Meanwhile, whatever happened in either of those rain scenarios Perez would still be well in front of Alonso and Hamilton becuase he had enough of a gap to cover them both, so Hamilton would only really be fighting for P2. This is all only if it did rain a fair amount as whilst you say it mostly isn't drizzle in Malaysia, it did only drizzle in the later stages of the actual race.
Hamilton and Perez were both closing on Alonso before and after he pitted so if Hamilton had pitted at least 1 lap earlier (lap 40) than he did, he would have gained 5 seconds on Perez and may have had the chance to challenge for P2 or P1, whilst being less vulnerable to Vettel behind. You're words were,
They played safe with Hamilton. If you're in 3rd position that's not unusual. You need the points for the championship. Waiting for potential rain would be high risk not safe as everyone else had pitted and were on faster tyres, so wouldn't it be more logical to choose a strategy that covers Vettel and gives Hamilton a chance to challenge both cars in front?