Smallpox and some of the other potential diseases could indeed be very nasty even for the industrialized world but in all probability they could eventually be brought under control.
You're right that it would ravage the Third World, which is where a lot of these people come from after all. Even in many of their oil-rich countries the wealth is extremely concentrated, with relatively little trickling down to the non-oil infrastructure or to the common man on the street. Almost always when the ruling classes want top-rate medical care they find some place in the West because there's nothing in their own countries.
I wouldn't give the Jihadis too much credit for understanding all this however. Many of them know about the Koran and terrorism and not much else; even of those who do, there are often amazing gaps in their knowledge. For example, although the 9/11 hijackers don't seem to have broadcast much (if any) of their operational plans, they took some huge risks that revealed startling gaps in their knowledge of covert tradecraft. Since they were coached by the people back in Afganistan that means that this lack of knowledge must be organization-wide, not just one or two of the peons. Presumably many of these deficiencies have now been corrected, but these people aren't necessarily the sharpest knives in the drawer if you catch my drift. They're just armed and very motivated.
....... and there's also the question of whether they'd care if they did understand. If they think that it will bring down the US they'd probably think losing half or 3/4 of their own people would be a fair trade.
Seriously. These guys play for keeps.