The fact that these factions hail from different galaxies is what's most telling. The Reapers wouldn't have mass relays set up, which would decrease their overall movement significantly. However, if they indoctrinated some spies and sent those in ahead of time to figure out where the Rakatan Empire's core was, and entered the galaxy from the closest side, they could still reach Rakata Prime in about 20 days with FTL travel alone (judging by the known speed of FTL travel compared to a map of the Star Wars galaxy). During this time, the Rakatan Empire could engage in hit and run maneuvers due to their objectively greater speed and with the Star Forge, they wouldn't have to worry about troop casualties that much, and would still have a formidable fighting force by the time the Reapers reached Rakata Prime.
This assumes the Reapers are going for a straight shot, however, which Reapers have almost never been known to do. They would likely follow their normal strategy for massive empires and created a rebel faction. If things go well, they could take the Star Forge out of commission, or even use it themselves before beginning any serious invasion. Even without the Star Forge, though, the Rakatan Empire should still have a very good military and industrial base.
Once the Reapers gain a foothold (which I'm assuming they'll be able to do, considering how well their indoctrination strategy tends to work) and take control of the Star Forge, their navy would be nearly unstoppable unless the Rakatan Empire could mount a sizable enough counter attack to defeat the entire Reaper force outright, or at least before they can make good use of the Star Forge. I'm not entirely sure just how large the Rakatan fleet would be, but considering that the Protheans weren't able to defeat the Reapers outright, I doubt they would stand a much better chance without the Star Forge.
Onto the topic of ground fighting, one of the biggest advantages the Rakatans have is the force. I think it's worth noting, however, that the force doesn't directly work against extra galactic beings (since they lack midichlorians). On the other hand, it's unclear if the process of creating husks would eliminate midichlorians (probably not), so while the force wouldn't work on the Reapers themselves or the first wave of husks that they would have brought with them, it's still possible that it could be used against husks made on site. Even with the force, they probably would only be slightly better versions of the Asari, who were defeated pretty soundly on their home planet. While the force would make them a more difficult foe than the Asari or even the Protheans, I still think their defeat after the loss of the Star Forge would just be a matter of time.
