How does a multicellular, eukaryotic body treat heat-resistant pathogenic bacteria? How does the said body treat heat-resistant pathogenic bacteria? If fever is the body's response to foreign microbial invasion, then what happens if the bacteria is heat-resistant but the body's own cells and enzymes start to denature due to the excess heat? Are there other mechanisms that the multicellular, eukaryotic body can use to defeat foreigners?

The usual 'heat resistant' bacteria or thermophiles are free living organisms with specific niche and are not pathogenic. Most pathogens are mesophiles and that is why they are grow in the body temperature. Spores are thermotolerant but spores are dormant and are not actively growing microbes.

Having said that, different mesophiles can have different levels of thermotolerance. Pyrexia (fever) is not necessarily a defensive mechanism and is more of a by-product of a systemic inflammatory response. Moreover bacteria are more tolerant to temperature changes than our body; there are definitely other mechanisms to combat infection. Read about innate and acquired immune response.