You as the author can decide where you want to place the commas or rest pause that your readers should follow. You can even break up the long sentence in two or three smaller sentences. Shorter sentences make it clearer and more obvious as to where to stop and start each passage.
1. By treating their elders well, parents send a message to their children that they too would like to be accorded that honor, respect and good treatment in old age.
2. By treating their elders well parents send a message to their children, that they too would like to be accorded that honor, respect and good treatment in old age.
3. By treating their elders well parents send a message to their children. That they too would like to be accorded that honor, respect and good treatment in old age. (2 SENTENCES)
4. By treating their elders well. Parents send a message to their children that they too would like. To be accorded that honor, respect and good treatment in old age. (3 SENTENCES)
5, 6, 7, 8. It's up to you to direct your readers. Those readers that actuall read punctuation.
Yes the first part of your sentence is too long and needs a rest or a comma. Between the words well and parents is a natural place to take a rest in reading.