From the original Hayabusa example it would seem that while preventing planetary contamination is obviously desirable, science can still be done on heavily contaminated samples (only about 0.1% of the returned sample was actually from the asteroid).
https://curator.jsc.nasa.gov/hayabusa/forms/hayabusasamplepolicy.pdf
Although the sampling mechanism did not work, thousands of 10 – 100 µm particles were found in one of the sample containers, apparently introduced during the spacecraft impact into the surface of the asteroid. Many of these particles are shown to be asteroidal grains by their chemistry and mineralogy, but they are mixed with contaminant particles from the spacecraft.
The Hayabusa samples are a unique and valuable collection, yet constitute less than one thousandth the expected mass of the returned sample. Typical samples allocated to Investigators will be on the order of 10 µm in size. Larger particles, reaching up to 100 µm in diameter, are very rare.
The retrieval process was also very rough, to say the least.
The asteroidal particles were observed as fine particles dispersed on the interior surface of the Hayabusa sample collector. Initial attempts to remove particles individually by micromanipulators were determined to be ineffective. So far, particles have been removed in two ways: gently swabbing a Teflon spatula along the surface of the collector and by simply tapping the collector and collecting particles that fell out. An unknown number of asteroidal particles remain in the collector.
Here is a extensive paper that goes over the entire process of Hayabusa 1, going into more detail on the sterilization and cleaning procedures, along with how they separated the material and prepared the samples.
https://onlinelibrary.wiley.com/doi/epdf/10.1111/maps.12027
For the real part of Hayabusa, the reentry capsule arrived at the curation facility on 18June 2010, 3 days after the reentry, and underwent a Hayabusa return sample curation in JAXA151series of processes, which we performed in the rehearsal. Within seven days after the capsule reentry, the sample container was introduced into clean chamber No. 1 and the inner pressure of the container was estimated to be between vacuum and atmospheric pressure based on the value of a series of sensors equipped in the sample opening system. Then, the sample container was opened in vacuum condition to recover residual gas in the chamber, although the result was that most gas was from the terrestrial atmosphere. The container was transferred to the transportation chamber in vacuum and the sample catcher was set to the catcher handling container and brought to clean chamber No. 2 in atmospheric pressure nitrogen condition.
Finally, here's a source that overviewed the quarantine plans for the Hayabusa 2 mission, which was classified as a Catagory V unrestricted return.
According to the most recent scientific knowledge combined, the Hayabusa-2 team considers the 1999 JU3 mission as Category-2 for the outbound and Category-5 “unrestricted” Earth return for the inbound.
Page 34 of the PDF has a flowchart used for determining such catagorization and comes to the conclusion that
No Special Containment Required Beyond What Is Needed for Scientific Purposes = “Unrestricted Earth Return”
Wikipedia has an overview on what these categories indicate:
https://en.wikipedia.org/wiki/Planetary_protection#Target_categories
Category V, Unrestricted Category V: “Earth-return missions from bodies deemed by scientific opinion to have no indigenous life forms.”
So for asteroids of similar type to the one targeted for Hayabusa 2, it would seem planetary protection procedures like quarantine would not be required.