That's an interesting angle on this debate. I hadn't considered looking at it that way. I'll give it a try:
Kipchoge marathon vs Bekele 5K/10K
Kipchoge broke the world record once and ran those two impressive exhibition time trials. On the all-time list, his best record-eligible performances rank 1st, 3rd, and 4th; that's 3 top-5 performances in the marathon. He has won Olympic gold in two different Games, he hasn't won any world championships, and he has won 9 majors across 7 different years (2014-2019, 2022).
Bekele broke the world record 4 times. On the all-time list, his best performances at 5K rank 2nd and 5th, and his best performances at 10K rank 2nd, 3rd, 5th, and 7th; that's 3 top-5 performances and another top 10 time in the 10K plus 2 more top-5 performances in the 5K. He has won Olympic gold in two different Games, he has won world championships in 4 other years, and he has won 23 Golden League/Diamond League/World Athletics Final races across 8 different years (2003, 2005-2009, 2011, 2013).
We can also look at their 5 best performances and how they stack up based on the World Athletics Scoring Tables:
Kipchoge's 5 best marathons:
2:01:39: 1303 points
2:02:37: 1286 points
2:02:40: 1285 points
2:03:05: 1278 points
2:03:32: 1270 points
Average points: 1284.4
Bekele's 5 best 5K/10K times:
26:17: 1295 points
12:37: 1294 points
26:20: 1290 points
12:40: 1283 points
26:25: 1281 points
Average points: 1288.6
Verdict: It's definitely close, but I believe Bekele has the edge because he has broken the world record on more than one occasion, more top-10 performances in the 10K than Kipchoge has in the marathon, major victories across more years, and a higher average point value for his top 5 performances. Kipchoge's best marathon performance is better than Bekele's best 10K, but Bekele's 2nd, 3rd, 4th, and 5th best performances in his specialty are all better than Kipchoge's in his.
Kipchoge 5K/10K vs Bekele marathon
Kipchoge does not have any top 10 times in the 5K or 10K, but he is the 7th fastest performer all-time in the 5K. He won that famous 5K world championship in 2003, and he won three other global medals across 3 more years. He also won 7 Golden League/Diamond League/World Athletics Final races across 5 years (2003-2005, 2008, 2010).
Bekele is the 2nd fastest marathoner of all time, and he has two top 10 times in the marathon, ranking 2nd and 10th. He hasn't won any Olympic or world championship medals, but he has won two marathon majors (2016 and 2019 Berlin) and has finished on the podium at three other majors: 2016 London, 2017 London, and 2021 Berlin.
Kipchoge's 5 best 5K/10K runs:
12:46: 1259 points
12:50: 1246 points
12:50: 1245 points
26:49: 1244 points
12:51: 1242 points
Average points: 1247.2
Bekele's 5 best marathons:
2:01:41: 1302 points
2:03:03: 1278 points
2:05:04: 1243 points
2:05:57: 1228 points
2:06:47: 1214 points
Average points: 1253.0
Verdict: I'd say a draw. Kipchoge's world championship, 3 other global championship medals, and 7 Golden League/Diamond League/World Athletics Final wins outrank Bekele's 5 marathon major podium finishes and absence of any global championship medals (I blame the Ethiopian federation's 2016 mistake for Bekele not having an Olympic medal in the marathon). On the other hand, looking at times and placement on the all-time top 10 lists favors Bekele. Bekele is the 2nd fastest marathoner ever while Kipchoge is "only" the 7th fastest at 5K. Bekele's 5 best marathon times have a higher average point value than Kipchoge's 5 best performances at 5K/10K. Plus Bekele's top 2 marathon times have much higher point values than anything Kipchoge did at 5/10. Overall, it's very close, basically a toss-up!
Summary and Additional Consideration
If we merely look at their track and marathon performances, it's very close. Bekele has the edge in his specialty events, and they're basically even in their non-specialties.
Of course, merely looking at their track and marathon performances omits an analysis of what they did in cross country, which should absolutely be considered a separate category. As I've stated previously, Bekele's quintuple-double at world cross is phenomenal. It is not a guarantee that someone who is great at 5K/10K on the track will also be great in cross country at the global level, or vice versa.
For proof, look at Haile Gebrselassie's finishes at World Cross:
1993: 7th
1994: 3rd
1996: 5th
Similarly, we can look at the other two modern day runners who have consistently dominated at cross country besides Bekele: Paul Tergat and Geoffrey Kamworor. They won a combined 0 (zero) gold medals on the track.
Track and cross country require different strengths. One involves running laps on a flat oval, the other requires running over hill and dale (and in mud). Bekele's ability to consistently dominate at both is exceptional. He should be recognized for this.