The role of Palpatine-Sidious in forming this conflict is highly exaggerated, although he did aid its development into an outright war, blackmailing the TF in the name of the crime syndicate "Black sun" and at the same time contacting the gungans with offers of armed and political aid. Despite that, it should be noted that the sides of the conflict dug completely on their own the hole into which Palpatine-Sidious later pushed them.
On this background, the secret arrival of Chancellor Valorum's envoys and the choosing of Jedi Knights for a seemingly routine bureaucratic mission become completely logical. Both sides of the conflict lied to the Senate and the government. Both sides had no desire for a public discussion about the nature of the problems. Both sides wanted the ambassadors to disappear as quickly as possible.
Palpatine-Sidious' Sith talents and his agents allowed him to discover and bring to TF and Naboo' attention all the details about the "embassy", their ship, course and the time when they were due to arrive. As a result, the Federation forces were fully prepared to meet them and the government of Naboo (the queen included) did nothing to aid the Jedi.
Unlike what was shown in the movie, the Jedi never made it to the TF station. Their ship was attacked and destroyed on the approach to the blockade forces. The crew, warned by the Jedi a few minutes before the attack, fled from the ship on three escape pods. Two of them were destroyed by the enemy ships. The Jedi Qui-Gon Jinn and Obi-Wan Kenobi (also known as "unlucky Ben") managed to destroy their pod's power grid (by cutting the wiring with their lightsabers) and went into trance, thus fooling the TF automatic interceptors. It was then that Obi-Wan said his famous phrase "The negotiations were short".
Not having even orbital velocity, the pod was naturally attracted to the planet. Upon entering the thicker layers of the atmosphere the reserve thrusters were activated which gave the Jedi a relatively soft landing