Mixing solder alloys on the same board is never a good idea, but it is a cleaver thought. It won't be long before we are all required to "get the lead out" so let's consider the real problem: getting enough heat into the Modules to let them solder safely along with your BGAs.
First, make sure you are profiling the temperatures of the critical parts, at least the BGAs (those parts at risk) and your "Mdules" (the parts that are not getting hot enough). This data will be critical in finding the best reflow recipe.
With convection reflow ovens, you have three options: higher temperature, higher convection rate (air flow), or more time, and combination of the three. Since over temperature of the BGAs is the main concern, I don't recommend higher temperatures in the zones. This just opens you up to the BGAs going well above their kill temp.
You can increase the convection (air flow rate) IF you have this option on your reflow oven. Some do, some don't. This takes the form of fan RPMs, fan frequency (Hz), PSI control, a Low, Medium, High setting and other recipe settings depending on the oven.
This increased setting will allow you to heat thermally massive parts without increasing the set point temperature in the zones. This lowers the risk of getting the BGAs too hot, because the zone temp is still the same, while pushing more heat into your Modules. It will force the BGAs to get up to temp faster, thus increasing their time above temp, so you should make sure this time limit is not violated.
If you can't increase the convection rate, either because you do not have the control, or it is already at maximum, then the final option is to increase the time in each zone. This is of course done by lowering the conveyor speed.
More time in each zone, again without increasing the zone temperature set points, will allow more time for the thermally massive Modules to get to the needed temp without risking the BGAs maximum temperature.
Again, this will increase the time the BGAs spend above temp, so this should be watch to make sure you are not violating this time limit.
Another approach is to "heat shield" the sensitive BGA with the same composite material used to make wave solder pallets. We make wave solder pallets to protect parts on the board from the wave, and we can do the same thing for reflow.
Make a reflow pallet that covers (top side) the BGAs and other sensitive components and protect them from the heat convection because it acts as an insulator to slow the heat rise for these parts. Yes, the "pallets" would have to be applied to every board being reflow soldered, however, they are reused 1000s of times, just like in wave soldering.
If you have already attempted these ideas, then it may be time to try a different reflow process, like Vapor Phase. This process can force heat into the heaviest of thermal masses without risking temperature sensitive components, because the maximum the parts will see temperature is controlled by the boiling point of the liquid used in the system, typically 230C or 240C.
It worth a renewed look at this older, but returning reflow process, now that new "ozone safe" liquids have been developed.